Swan Populations Grow 30 Times Faster in Nature Reserves

Sea temperatures control the distributions of european marine fish, to help dry forests, fire needs to be just the right intensity, and happen more than once, plant roots fuel tropical soil animal communities, phone-based measurements provide fast, accurate information about the health of forests, deforestation in the tropics linked to a reduction in rainfall, a fifth of california's sierra nevada conifer forests are stranded in habitats that have grown too warm for them, flower power: the role of ants in forest regeneration, australia's rarest bird of prey disappearing at alarming rate, new study reveals biodiversity loss drove ecological collapse after the 'great dying', rising river temperatures hold important clues about climate and other human impacts, urban ponds require attention to ensure biodiversity.

New Research Reveals 12 Ways Aquaculture Can Benefit the Environment

Climate 'Spiral' Threatens Land Carbon Stores

ecology research articles

Excitement that Inspires

Ecology 2739 articles archived since 1845

ecology research articles

We Must Stop Treating Grasslands as Wastelands

The grasslands of India and elsewhere do not need to have economic value to be worth studying and preserving

ecology research articles

Pablo Escobar’s ‘Cocaine Hippos’ Spark Conservation Fight

Researchers worry the Colombian environmental ministry will side with animal-rights activists rather than curb the spread of invasive hippos once kept by drug-cartel leader Pablo Escobar...

ecology research articles

Do Trees Really Support Each Other through a Network of Fungi?

Trees communicate and cooperate through a fungal web, according to a widespread idea. But not everyone is convinced

ecology research articles

A ‘De-extinction’ Company Wants to Bring Back the Dodo

A de-extinction company known for its plans to resurrect the mammoth and Tasmanian tiger has announced it will also bring back the dodo

ecology research articles

Rare Animals’ Microbiomes Harbor Survival Secrets

Scientists are beginning to decode endangered creatures’ microbial ecosystems

ecology research articles

How the Moon Devastated a Mangrove Forest

In 2015 the moon’s wobble and an El Niño teamed up to kill off tens of millions of Australian mangroves

ecology research articles

9 Science Stories That Restore Our Faith in Humanity

A river’s “gut” revived, snake-saving social media, an intragalactic donut, and more success stories of the year

ecology research articles

Global Population Growth Is Slowing Down. Here’s One Reason Why

In 2022 the world’s population hit the eight-billion mark. But such milestones could top out by the end of the century

ecology research articles

Plants Call in Hornets to Rescue Their Seeds

These trees trick hornets with the promise of a scrumptious caterpillar buffet

ecology research articles

News Briefs from around the World: October 2022

In case you missed it

ecology research articles

Poem: ‘Diptych: Abscission and Marcescence’

Science in meter and verse

ecology research articles

Vultures Prevent Tens of Millions of Metric Tons of Carbon Emissions Each Year

Vultures get a bad reputation for their carrion-scavenging ways, but their dietary habits prevent the release of greenhouse gases

ecology research articles

Parasites Are Choosy about Where They Live

Intestinal parasites infect herbivores with similar digestive systems

ecology research articles

De-extinction Company Aims to Resurrect the Tasmanian Tiger

The scientists who want to bring back mammoths now hope to revive the marsupial carnivore thylacine

ecology research articles

Shrimp Sounds Could Lure Baby Oysters to Build New Reefs

Piping in audio of snapping shrimp could help the oysters reestablish long-lost ecosystems

ecology research articles

50, 100 & 150 Years Ago: August 2022

Creation as science; climbing Mount Everest

ecology research articles

The Beaver Emerges as a ‘Climate-Solving Hero’

Dam-building beavers are helping stave off some of the worst effects of climate-driven droughts and floods

ecology research articles

How Culturally Significant Mammals Tell the Story of Social Ascension for Black Americans

Juneteenth offers an opportunity to reflect on the wildlife linked to a people’s transformation

ecology research articles

Redwoods Grow Weird Leaves to Suck Water from Air

Here’s how they choose the right leaf for the job

ecology research articles

Wiggling Whiskers Help Hungry Seals Hunt in the Dark

A new seal’s-eye view shows these specialized hairs in motion at sea

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Page 1 of 5

Northward expansion trends and future potential distribution of a dragonfly Ischnura senegalensis Rambur under climate change using citizen science data in South Korea

Citizen science is becoming a mainstream approach of baseline data collection to monitor biodiversity and climate change. Dragonflies (Odonata) have been ranked as the highest priority group in biodiversity mo...

Morphological variables restrict flower choice of Lycaenid butterfly species: implication for pollination and conservation

Butterflies make an important part for plant-pollinator guild. These are nectar feeder or occasionally pollen feeder and thus proboscis of the butterfly species are considered as one of the most important vari...

Honey bees and their brood: a potentially valuable resource of food, worthy of greater appreciation and scientific attention

Despite the consumption of bee brood in several parts of the world, particularly in the tropical areas, the practice has received comparatively little attention. We have reviewed all the available information ...

Attributes and references to honey bees (Insecta; Hymenoptera; Apidae) and their products in some Asian and Australian societies’ folkloristic domains

References to insects in myths, stories, and idioms can be found in almost any culture, but with regard to references involving honey bee species in the Asia-Australian region, little information is available....

RETRACTED ARTICLE: Major environmental factors and traits of invasive alien plants determining their spatial distribution

As trade increases, the influx of various alien species and their spread to new regions are prevalent and no longer a special problem. Anthropogenic activities and climate changes have made the distribution of...

Spatial distribution of halophytes and environment factors in salt marshes along the eastern Yellow Sea

Salt marshes provide a variety of ecosystem services; however, they are vulnerable to human activity, water level fluctuations, and climate change. Analyses of the relationships between plant communities and e...

PollMap: a software for crop pollination mapping in agricultural landscapes

Ecosystem service mapping is an important tool for decision-making in landscape planning and natural resource management. Today, pollination service mapping is based on the Lonsdorf model (InVEST software) tha...

Current status of alert alien species management for the establishment of proactive management systems in Korea

Some of the introduced alien species introduced settle, multiply, and spread to become invasive alien species (IAS) that threaten biodiversity. To prevent this, Korea and other countries legally designate and ...

Dust and sandstorm: ecosystem perspectives on dryland hazards in Northeast Asia: a review

A review of the literature was carried out to study dust and sandstorm (DSS) in terms of its ecosystem processes and relationship to other dryland disasters in Northeast Asia. Drylands are ecosystems that incl...

Changes in nocturnal insect communities in forest-dominated landscape relevant to artificial light intensity

Artificial light at night has recently been identified as a major factor adversely affecting global insect diversity. Here, we compared the insect diversity in Gwangneung Forest Biosphere Reserve, specifically...

Occurrence and diet analysis of sea turtles in Korean shore

Sea turtles, which are globally endangered species, have been stranded and found as bycatch on the Korean shore recently. More studies on sea turtles in Korea are necessary to aid their conservation. To invest...

Quantifying how urban landscape heterogeneity affects land surface temperature at multiple scales

Landscape metrics have been widely applied to quantifying the relationship between land surface temperature and urban spatial patterns and have received acceptable verification from landscape ecologists but so...

The relationship of mean temperature and 9 collected butterfly species’ wingspan as the response of global warming

Organism body size is a basic characteristic in ecology; it is related to temperature according to temperature-size rule. Butterflies are affected in various aspects by climate change because they are sensitiv...

Non-deep physiological dormancy in seeds of Euphorbia jolkinii Boiss. native to Korea

Euphorbia jolkinii Boiss. is a perennial species native to Jeju Island and the southern coastal area of Korea. Particularly on Jeju Island, the yellow flowers of E. jolkinii Boiss. have a high ornamental value be...

Predation of the Japanese keelback ( Hebius vibakari Boie, 1826) by the Slender racer ( Orientocoluber spinalis Peters, 1866)

The Slender racer ( Orientocoluber spinalis Peters, 1866) has recently been reclassified to the new genus Orientocoluber from Hierophis . Ecological knowledge of this species is limited due to its highly mobile beh...

Major environmental factors and traits of invasive alien plants determine their spatial distribution: a case study in Korea

As trade increases, the influx of various alien species and their spread to new regions are prevalent, making them a general problem globally. Anthropogenic activities and climate change have led to alien spec...

Distribution and habitat use of the endangered Siberian flying squirrel Pteromys volans (Rodentia: Sciuridae)

Understanding the habitat characteristics of the endangered Siberian flying squirrel Pteromys volans is the first step in conserving and managing the forests it requires for nesting, gliding, and feeding. Therefo...

How effective are artificial nests in attracting bees? A review

Recent declines in bee populations, along with increasing demand for pollination services in urban, agricultural, and natural environments, have led to strategies to attract wild bees to these areas. One of th...

Tissue-specific systemic responses of the wild tobacco Nicotiana attenuata against stem-boring herbivore attack

Plants are able to optimize defense responses induced by various herbivores, which have different feeding strategies. Local and systemic responses within a plant after herbivory are essential to modulate herbi...

Estimating potential range shift of some wild bees in response to climate change scenarios in northwestern regions of Iran

Climate change is occurring rapidly around the world, and is predicted to have a large impact on biodiversity. Various studies have shown that climate change can alter the geographical distribution of wild bee...

Trends in the effects of climate change on terrestrial ecosystems in the Republic of Korea

In this review, we aimed to synthesize the current knowledge on the observed and projected effects of climate change on the ecosystems of Korea (i.e., the Republic of Korea (ROK) or South Korea), as well as th...

Principle of restoration ecology reflected in the process creating the National Institute of Ecology

The creation of the National Institute of Ecology began as a national alternative project to preserve mudflats instead of constructing the industrial complexes by reclamation, and achieve regional development....

Small-scale spatial genetic structure of Asarum sieboldii metapopulation in a valley

Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short se...

Diel and seasonal activity pattern of alien sika deer with sympatric mammalian species from Muljangori-oreum wetland of Hallasan National Park, South Korea

Sika deer, Cervus nippon , were originally introduced to South Korea from Japan and Taiwan for commercial farming purposes. Unfortunately, they were released into the wild during religious events and have since be...

Effects of different day length and wind conditions to the seedling growth performance of Phragmites australis

To understand shade and wind effects on seedling traits of common reed ( Phragmites australis ), we conducted a mesocosm experiment manipulating day length (10 h daytime a day as open canopy conditions or 6 h dayti...

Categorized wetland preference and life forms of the vascular plants in the Korean Peninsula

In 2020, a categorized list of wetland preferences, major habitats, and life forms of 4145 vascular plant taxa occurring in the Korean Peninsula was published by the National Institute of Biological Resources....

Elevational distribution ranges of vascular plant species in the Baekdudaegan mountain range, South Korea

The climate is changing rapidly, and this may pose a major threat to global biodiversity. One of the most distinctive consequences of climate change is the poleward and/or upward shift of species distribution ...

Study on the photosynthetic characteristics of Eutrema japonica (Siebold) Koidz. under the pulsed LEDs for simulated sunflecks

The sunfleck is an important light environmental factor for plants that live under the shade of trees. Currently, the smartfarm has a system that can artificially create these sunfleks. Therefore, it was inten...

Influence of trees and associated variables on soil organic carbon: a review

The level of soil organic carbon (SOC) fluctuates in different types of forest stands: this variation can be attributed to differences in tree species, and the variables associated with soil, climate, and topo...

Comparison of ecophysiological and leaf anatomical traits of native and invasive plant species

To address the lack of evidence supporting invasion by three invasive plant species ( Imperata cylindrica, Lantana camara, and Chromolaena odorata ) in tropical ecosystems, we compared the ecophysiological and leaf...

Effects of soil water content and light intensity on the growth of Molinia japonica in montane wetlands in South Korea

Montane wetlands are unique wetland ecosystems with distinct physicochemical characteristics, and Molinia japonica often makes dominant communities in montane wetlands in South Korea. In order to figure out the e...

First detection of ranavirus in a wild population of Dybowski’s brown frog ( Rana dybowskii ) in South Korea

Ranavirus is an emerging infectious disease which has been linked to mass mortality events in various amphibian species. In this study, we document the first mass mortality event of an adult population of Dybo...

Cushion plant Silene acaulis is a pioneer species at abandoned coal piles in the High Arctic, Svalbard

Abandoned coal piles after the closure of mines have a potential negative influence on the environment, such as soil acidification and heavy metal contamination. Therefore, revegetation by efficient species is...

Vegetation structure and distribution characteristics of Symplocos prunifolia , a rare evergreen broad-leaved tree in Korea

In Korea, Symplocos prunifolia Siebold. & Zucc. is only found on Jeju Island. Conservation of the species is difficult because little is known about its distribution and natural habitat. The lack of research and ...

Growth performance of planted population of Pinus roxburghii in central Nepal

Climate change has altered the various ecosystem processes including forest ecosystem in Himalayan region. Although the high mountain natural forests including treelines in the Himalayan region are mainly repo...

Correction to: Application of smart mosquito monitoring traps for the mosquito forecast systems by Seoul Metropolitan city

An amendment to this paper has been published and can be accessed via the original article.

The original article was published in Journal of Ecology and Environment 2020 44 :13

Correction to: Effect of precipitation on soil respiration in a temperate broad-leaved forest

The original article was published in Journal of Ecology and Environment 2018 42 :10

Effects of cutting and sowing seeds of native species on giant ragweed invasion and plant diversity in a field experiment

Ambrosia trifida is a highly invasive annual plant, but effective control methods have not been proposed. Among various eradication methods, cutting is a simple measure to control invasive plants, and sowing seed...

Mid-term (2009-2019) demographic dynamics of young beech forest in Albongbunji Basin, Ulleungdo, South Korea

The stem exclusion stage is a stage of forest development that is important for understanding the subsequent understory reinitiation stage and maturation stage during which horizontal heterogeneity is formed. ...

Annual and spatial variabilities in the acorn production of Quercus mongolica

Genus Quercus is a successful group that has occupied the largest area of forest around the world including South Korea. The acorns are an important food source for both wild animals and humans. Although the repr...

Prevalence of Puccinia abrupta var. partheniicola and its impact on Parthenium hysterophorus in Kathmandu Valley, Nepal

Parthenium hysterophorus is a noxious invasive weed in tropical and subtropical regions of the world, including Nepal. Among 11 species of biological control agents released to control P. hysterophorus in Ausrtal...

Ecological impact of fast industrialization inferred from a sediment core in Seocheon, West Coast of Korean Peninsula

Rapid industrialization has caused various impacts on nature, including heavy metal pollution. However, the impacts of industrialization vary depending on the types of industrializing activity and surrounding ...

Influence of roadkill during breeding migration on the sex ratio of land crab ( Sesarma haematoche )

Adult land crabs generally live on land while their larvae live in the sea. In the case of Sesarma haematoche , female crabs migrate from land to sea to release the larvae at the high tide of syzygy night. Artific...

Population structure and regeneration of Himalayan endemic Larix species in three high-altitude valleys in Nepal Himalaya

The Himalayan forests are of great importance to sustain the nature and community resource demands. These forests are facing pressures both from anthropogenic activities and ongoing global climatic changes. Po...

Otolith microchemistry reveals the migration patterns of the flathead grey mullet Mugil cephalus (Pisces: Mugilidae) in Korean waters

The flathead grey mullet Mugil cephalus has the widest distribution among mugilid species. Recent studies based on mitochondrial DNA sequences showed that the species comprises at least 14 different groups, three...

Population size, group and age structure of geladas ( Theropithecus gelada ) in escarpments of Eastern Tigray, Ethiopia: implication for conservation

Geladas ( Theropithecus gelada ), endemic to Ethiopia, are distributed closely related to the escarpments and gorge systems of the country, and large populations are found in the Simien Mountain National Park. This...

Coexistence of plant species under harsh environmental conditions: an evaluation of niche differentiation and stochasticity along salt marsh creeks

Ecologists have achieved much progress in the study of mechanisms that maintain species coexistence and diversity. In this paper, we reviewed a wide range of past research related to these topics, focusing on ...

Re-emergence of the Glossy Ibis ( Plegadis falcinellus ) in inland South Korea

Glossy Ibis ( Plegadis falcinellus ), which has never been recorded in South Korea, appeared on Jeju Island in 2018 and re-emerged in the inland area of Seocheon-gun (South Chungcheong Province) and in Goyang-si (G...

Diet composition of the Korean wild boar Sus scrofa coreanus (Suidae) at Mt. Jeombongsan, Korea

Korean wild boars ( Sus scrofa coreanus Heude), because of their adaptability, are a widespread large mammal; however, they sometimes cause problems by invading farms and eating the crops, creating insufficiencies...

Review on the succession process of Pinus densiflora forests in South Korea: progressive and disturbance-driven succession

Most of the Pinus densiflora forests, occupying the largest area, have been restored in South Korea since the 1970s. As young pioneer forests, the succession process is under way. Since the forests are distribute...

Journal of Ecology and Environment

ISSN: 2288-1220

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Ecology publishes articles that report on the basic elements of ecological research. Emphasis is placed on concise, clear articles documenting important ecological phenomena. The journal publishes a broad array of research that includes a rapidly expanding envelope of subject matter, techniques, approaches, and concepts: paleoecology through present-day phenomena; evolutionary, population, physiological, community, and ecosystem ecology, as well as biogeochemistry; inclusive of descriptive, comparative, experimental, mathematical, statistical, and interdisciplinary approaches.

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ecology research articles

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Collection  10 March 2022

Top 100 in Ecology

This collection highlights our most downloaded* ecology papers published in 2021. Featuring authors from aroud the world, these papers showcase valuable research from an international community.

*Data obtained from SN Insights which is based on Digital Science's Dimensions.

image of a turtle swimming surrounded by a school of fish

The first true millipede—1306 legs long

ecology research articles

Lethal coalitionary attacks of chimpanzees ( Pan troglodytes troglodytes ) on gorillas ( Gorilla gorilla gorilla ) in the wild

ecology research articles

Defining priority areas for blue whale conservation and investigating overlap with vessel traffic in Chilean Patagonia, using a fast-fitting movement model

ecology research articles

Earliest evidence of herd-living and age segregation amongst dinosaurs

ecology research articles

Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons

ecology research articles

Excess protein enabled dog domestication during severe Ice Age winters

ecology research articles

Honey bee hives decrease wild bee abundance, species richness, and fruit count on farms regardless of wildflower strips

ecology research articles

Tracking late Pleistocene Neandertals on the Iberian coast

ecology research articles

Exposure to foreign gut microbiota can facilitate rapid dietary shifts

ecology research articles

Self-care tooling innovation in a disabled kea ( Nestor notabilis )

ecology research articles

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan

ecology research articles

Microplastics in fish and fishmeal: an emerging environmental challenge?

ecology research articles

An Italian dinosaur Lagerstätte reveals the tempo and mode of hadrosauriform body size evolution

ecology research articles

Seagrasses provide a novel ecosystem service by trapping marine plastics

ecology research articles

Mistaken identity may explain why male sea snakes ( Aipysurus laevis , Elapidae, Hydrophiinae) “attack” scuba divers

ecology research articles

Explainable identification and mapping of trees using UAV RGB image and deep learning

ecology research articles

The giant panda is cryptic

ecology research articles

Pivot burrowing of scarab beetle ( Trypoxylus dichotomus ) larva

ecology research articles

Redefining the oceanic distribution of Atlantic salmon

ecology research articles

Chest beats as an honest signal of body size in male mountain gorillas ( Gorilla beringei beringei )

ecology research articles

Powered flight in hatchling pterosaurs: evidence from wing form and bone strength

ecology research articles

Two wild female bonobos adopted infants from a different social group at Wamba

ecology research articles

Multiple pygmy blue whale acoustic populations in the Indian Ocean: whale song identifies a possible new population

ecology research articles

Action potentials induce biomagnetic fields in carnivorous Venus flytrap plants

ecology research articles

North Pacific warming shifts the juvenile range of a marine apex predator

ecology research articles

Spatial and temporal pattern of wildfires in California from 2000 to 2019

ecology research articles

Effects of climate change and land cover on the distributions of a critical tree family in the Philippines

ecology research articles

African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning

ecology research articles

Russian forest sequesters substantially more carbon than previously reported

ecology research articles

Isotope data from amino acids indicate Darwin’s ground sloth was not an herbivore

ecology research articles

Late Pleistocene human paleoecology in the highland savanna ecosystem of mainland Southeast Asia

ecology research articles

Early Pleistocene faunivorous hominins were not kleptoparasitic, and this impacted the evolution of human anatomy and socio-ecology

ecology research articles

An ecological niche shift for Neanderthal populations in Western Europe 70,000 years ago

ecology research articles

Surface slicks are pelagic nurseries for diverse ocean fauna

ecology research articles

Field measurements of a massive Porites coral at Goolboodi (Orpheus Island), Great Barrier Reef

ecology research articles

Ongoing ecological and evolutionary consequences by the presence of transgenes in a wild cotton population

ecology research articles

Novel and disappearing climates in the global surface ocean from 1800 to 2100

ecology research articles

Partial shading by solar panels delays bloom, increases floral abundance during the late-season for pollinators in a dryland, agrivoltaic ecosystem

ecology research articles

The early hunting dog from Dmanisi with comments on the social behaviour in Canidae and hominins

ecology research articles

Comprehensive comparative morphology and developmental staging of final instar larvae toward metamorphosis in the insect order Odonata

ecology research articles

G enome-wide data implicate terminal fusion automixis in king cobra facultative parthenogenesis

ecology research articles

New evidence from exceptionally “well-preserved” specimens sheds light on the structure of the ammonite brachial crown

ecology research articles

Population decline in a ground-nesting solitary squash bee ( Eucera pruinosa ) following exposure to a neonicotinoid insecticide treated crop ( Cucurbita pepo )

ecology research articles

Tropical deforestation induces thresholds of reproductive viability and habitat suitability in Earth’s largest eagles

ecology research articles

Biodiversity and ecosystem functions depend on environmental conditions and resources rather than the geodiversity of a tropical biodiversity hotspot

ecology research articles

Summer weather conditions influence winter survival of honey bees ( Apis mellifera ) in the northeastern United States

ecology research articles

Evidence that spillover from Marine Protected Areas benefits the spiny lobster ( Panulirus interruptus ) fishery in southern California

ecology research articles

Metal concentrations in coastal sharks from The Bahamas with a focus on the Caribbean Reef shark

ecology research articles

First tracks of newborn straight-tusked elephants ( Palaeoloxodon antiquus )

ecology research articles

An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico ) from the arc of deforestation

ecology research articles

eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

ecology research articles

Large-scale variations in the dynamics of Amazon forest canopy gaps from airborne lidar data and opportunities for tree mortality estimates

ecology research articles

Tipping point realized in cod fishery

ecology research articles

Temporal activity patterns suggesting niche partitioning of sympatric carnivores in Borneo, Malaysia

ecology research articles

No evidence of physiological declines with age in an extremely long-lived fish

ecology research articles

International fisheries threaten globally endangered sharks in the Eastern Tropical Pacific Ocean: the case of the Fu Yuan Yu Leng 999 reefer vessel seized within the Galápagos Marine Reserve

ecology research articles

Indirect effects of invasive rat removal result in recovery of island rocky intertidal community structure

ecology research articles

Assessing the carbon capture potential of a reforestation project

ecology research articles

The evolutionary history of manatees told by their mitogenomes

ecology research articles

Microplastics accumulate fungal pathogens in terrestrial ecosystems

ecology research articles

Advances in automatic identification of flying insects using optical sensors and machine learning

ecology research articles

Aboveground plant-to-plant communication reduces root nodule symbiosis and soil nutrient concentrations

ecology research articles

The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions

ecology research articles

Highest risk abandoned, lost and discarded fishing gear

ecology research articles

Future thermal regimes for epaulette sharks ( Hemiscyllium ocellatum ): growth and metabolic performance cease to be optimal

ecology research articles

Earliest evidence of marine habitat use by mammals

ecology research articles

Constraining the chronology and ecology of Late Acheulean and Middle Palaeolithic occupations at the margins of the monsoon

ecology research articles

Neonicotinoids disrupt memory, circadian behaviour and sleep

ecology research articles

Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage

ecology research articles

Ecosystem response persists after a prolonged marine heatwave

ecology research articles

Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling

ecology research articles

Camera trap placement for evaluating species richness, abundance, and activity

ecology research articles

Assessing biophysical and socio-economic impacts of climate change on regional avian biodiversity

ecology research articles

Smell of green leaf volatiles attracts white storks to freshly cut meadows

ecology research articles

Dinosaur senescence: a hadrosauroid with age-related diseases brings a new perspective of “old” dinosaurs

ecology research articles

Positive effects of COVID-19 lockdown on river water quality: evidence from River Damodar, India

ecology research articles

Snow algae blooms are beneficial for microinvertebrates assemblages (Tardigrada and Rotifera) on seasonal snow patches in Japan

ecology research articles

Coastal wetlands can be saved from sea level rise by recreating past tidal regimes

ecology research articles

Identifying unknown Indian wolves by their distinctive howls: its potential as a non-invasive survey method

ecology research articles

Optimal fishing effort benefits fisheries and conservation

ecology research articles

The spreading of the invasive sacred ibis in Italy

ecology research articles

Exceptional fossil assemblages confirm the existence of complex Early Triassic ecosystems during the early Spathian

ecology research articles

Allelopathic effect of Artemisia argyi on the germination and growth of various weeds

ecology research articles

Organophosphate poisoning of Hyacinth Macaws in the Southern Pantanal, Brazil

ecology research articles

The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes

ecology research articles

Novel approach to enhance coastal habitat and biotope mapping with drone aerial imagery analysis

ecology research articles

High resolution biologging of breaching by the world’s second largest shark species

ecology research articles

The largest hoplophonine and a complex new hypothesis of nimravid evolution

ecology research articles

Dangerous demographics in post-bleach corals reveal boom-bust versus protracted declines

ecology research articles

Welwitschia : Phylogeography of a living fossil, diversified within a desert refuge

ecology research articles

Response of bacterial and fungal communities to high petroleum pollution in different soils

ecology research articles

Integrating multiple chemical tracers to elucidate the diet and habitat of Cookiecutter Sharks

ecology research articles

Environmental stressors, complex interactions and marine benthic communities’ responses

ecology research articles

eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

ecology research articles

Distance sampling surveys reveal 17 million vertebrates directly killed by the 2020’s wildfires in the Pantanal, Brazil

ecology research articles

Description of five new species of the Madagascan flagship plant genus Ravenala (Strelitziaceae)

ecology research articles

A symbiotic aphid selfishly manipulates attending ants via dopamine in honeydew

ecology research articles

Ixodiphagus hookeri wasps (Hymenoptera: Encyrtidae) in two sympatric tick species Ixodes ricinus and Haemaphysalis concinna (Ixodida: Ixodidae) in the Slovak Karst (Slovakia): ecological and biological considerations

ecology research articles

Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

ecology research articles

Timely poacher detection and localization using sentinel animal movement

Quick links

ecology research articles

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Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases

Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) ...

Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities

Diatoms are present in all waters and are highly sensitive to pollution gradients. Therefore, they are ideal bioindicators for water quality assessment. Current indices used in these applications are based on ...

Conifers and non-native tree species shift trophic niches of generalist arthropod predators in Central European beech forests

Functional diversity is vital for forest ecosystem resilience in times of climate-induced forest diebacks. Admixing drought resistant non-native Douglas fir, as a partial replacement of climate-sensitive Norwa...

Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex

Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complica...

Complexity vs linearity: relations between functional traits in a heterotrophic protist

Functional traits are phenotypic traits that affect an organism’s performance and shape ecosystem-level processes. The main challenge when using functional traits to quantify biodiversity is to choose which on...

Environmental implications of Ptolemaic Period rodents and shrews from the Sacred Falcon Necropolis at Quesna, Egypt (Mammalia: Muridae and Soricidae)

Assemblages of mummified and preserved animals in necropoleis of Ptolemaic Period Egypt (ca. 332–30 BC) document some aspects of the ceremonial and religious practices of the ancient Egyptians, but study of th...

Ecological and biogeographic features shaped the complex evolutionary history of an iconic apex predator ( Galeocerdo cuvier )

The tiger shark ( Galeocerdo cuvier ) is a large iconic marine predator inhabiting worldwide tropical and subtropical waters. So far, only mitochondrial markers and microsatellites studies have investigated its wor...

Unparalleled details of soft tissues in a Cretaceous ant

For social insects such as ants, the internal organs are likely important in understanding their eusocial behavior and evolution. Such organs, however, are rarely preserved on fossils. In each of the few cases...

Unravelling the palaeobiogeographical history of the living fossil genus Rehderodendron (Styracaceae) with fossil and extant pollen and fruit data

The relict genus Rehderodendron (Styracaceae), the species of which are restricted to mostly warm temperate to tropical climate in East Asia today, is known from fossil fruits and pollen in Europe during warmer p...

Response of arboreal Collembola communities to the conversion of lowland rainforest into rubber and oil palm plantations

In the last decades, Southeast Asia has experienced massive conversion of rainforest into rubber and oil palm monoculture plantations. The effects of this land-use change on canopy arthropods are still largely...

An insight into cancer palaeobiology: does the Mesozoic neoplasm support tissue organization field theory of tumorigenesis?

Neoplasms are common across the animal kingdom and seem to be a feature plesiomorphic for metazoans, related with an increase in somatic complexity. The fossil record of cancer complements our knowledge of the...

Cell size, body size and Peto’s paradox

Carcinogenesis is one of the leading health concerns afflicting presumably every single animal species, including humans. Currently, cancer research expands considerably beyond medicine, becoming a focus in ot...

Allopatric divergence of cooperators confers cheating resistance and limits effects of a defector mutation

Social defectors may meet diverse cooperators. Genotype-by-genotype interactions may constrain the ranges of cooperators upon which particular defectors can cheat, limiting cheater spread. Upon starvation, the...

Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis

The number of interactions between a transferable gene or its protein product and genes or gene products native to its microbial host is referred to as connectivity. Such interactions impact the tendency of th...

Fruit scent as an honest signal for fruit quality

Fleshy fruits evolved to be attractive to seed dispersers through various signals such as color and scent. Signals can evolve through different trajectories and have various degrees of reliability. The stronge...

Evidence for a chemical arms race between cuckoo wasps of the genus Hedychrum and their distantly related host apoid wasps

Brood parasites can exert strong selection pressure on their hosts. Many brood parasites escape their detection by mimicking sensory cues of their hosts. However, there is little evidence whether or not the ho...

A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

Allegheny woodrats ( Neotoma magister ) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling...

Modeling the metabolic evolution of mixotrophic phytoplankton in response to rising ocean surface temperatures

Climate change is expected to lead to warming in ocean surface temperatures which will have unequal effects on the rates of photosynthesis and heterotrophy. As a result of this changing metabolic landscape, di...

Land use and soil characteristics affect soil organisms differently from above-ground assemblages

Land-use is a major driver of changes in biodiversity worldwide, but studies have overwhelmingly focused on above-ground taxa: the effects on soil biodiversity are less well known, despite the importance of so...

Genetic diversity and family groups detected in a coyote population with red wolf ancestry on Galveston Island, Texas

Hybridization can be a conservation concern if genomic introgression leads to the loss of an endangered species’ unique genome, or when hybrid offspring are sterile or less fit than their parental species. Yet...

Host-plant adaptation as a driver of incipient speciation in the fall armyworm ( Spodoptera frugiperda )

Divergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and ...

Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9

The arms race between humans and pathogens drives the evolution of the human genome. It is thus expected that genes from the interferon-regulatory factors family (IRFs), a critical family for anti-viral immune...

Unveiling a hotspot of genetic diversity in southern Italy for the endangered Hermann’s tortoise Testudo hermanni

Hotspots of intraspecific genetic diversity represent invaluable resources for species to cope with environmental changes, and their identification is increasingly recognized as a major goal of conservation ec...

Assessing soil microbes that drive fairy ring patterns in temperate semiarid grasslands

Fairy rings occur in diverse global biomes; however, there is a critical knowledge gap regarding drivers of fairy rings in grassland ecosystems. Grassland fairy rings are characterized belowground by an expand...

Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification

Detecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the...

Morphospecies and molecular diversity of ‘lace corals’: the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago

As in most bryozoans, taxonomy and systematics of species in the genus Reteporella Busk, 1884 (family Phidoloporidae) has hitherto almost exclusively been based on morphological characters. From the central North...

Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation

The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecesso...

Population dynamics and demographic history of Eurasian collared lemmings

Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming ( Dicrostonyx torquatus ) is a keystone species in...

Species and genetic diversity relationships in benthic macroinvertebrate communities along a salinity gradient

Species- and genetic diversity can change in parallel, resulting in a species-genetic diversity correlation (SGDC) and raising the question if the same drivers influence both biological levels of diversity. Th...

Sex-specific effects of inbreeding on body colouration and physiological colour change in the cichlid fish Pelvicachromis taeniatus

Colour expression is highly variable in animals. In fishes, rapid colour change, i.e. physiological colour change, can be observed in multiple contexts, e.g. in camouflage or communication, and is affected by ...

Insertion/deletion hotspots in the Nsp2, Nsp3, S1, and ORF8 genes of SARS-related coronaviruses

The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains many insertions/deletions (indels) from the genomes of other SARS-related coronaviruses. Some of the identified indels have r...

Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit

Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryo...

Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax )

Anadromous rainbow smelt ( Osmerus mordax ) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecol...

Gut microbiota differs between two cold-climate lizards distributed in thermally different regions

The metabolic cold-climate adaption hypothesis predicts that animals from cold environments have relatively high metabolic rates compared with their warm-climate counterparts. However, studies testing this hyp...

Phylogenetic divergences in brown rot fungal pathogens of Monilinia species from a worldwide collection: inferences based on the nuclear versus mitochondrial genes

Phylogenetic analyses for plant pathogenic fungi explore many questions on diversities, relationships, origins, and divergences of populations from different sources such as species, host, and geography. This ...

Reconstructing the neuromuscular ground pattern of phylactolaemate bryozoans: new data from the Lophopodidae

The solely freshwater inhabiting Phylactolaemata is a sister taxon to all other bryozoans. Among phylactolaemates, Lophopodidae represents an early branching clade that is therefore crucial for ground pattern ...

A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad ( Bombina orientalis ) in Beijing

The successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad ( Bombina orientalis ) p...

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Aggression is observed across the animal kingdom, and benefits animals in a number of ways to increase fitness and promote survival. While aggressive behaviors vary widely across populations and can evolve as ...

Polyandrous females but not monogamous females vary in reproductive ageing patterns in the bean bug Riptortus pedestris

In general, reproductive performance exhibits nonlinear changes with age. Specifically, reproductive performance increases early in life, reaches a peak, and then declines later in life. Reproductive ageing pa...

Prevalence of co-infection and genetic diversity of avian haemosporidian parasites in two rehabilitation facilities in Iran: implications for the conservation of captive raptors

Various haemosporidian parasites infect raptors, especially captive hosts who may be more exposed. Diagnosis of threatening factors such as infectious diseases indirectly has a significant role in protecting e...

Humans-livestock predators conflict in the Central and Eastern Part of Bale Mountains National Park, Ethiopia

Sharing of space by humans and wildlife at a time may ignite apparent conflict. Populations of many species are declining due to the degradation of wildlife habitats caused by agricultural activities. Addition...

The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera)

Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geo...

Does exclosure restore woody species regeneration in degraded lands? The case of Loma Bosa District of Dawuro zone, Southwestern Ethiopia

Exclosure becomes popular as a naming of the practice of excluding degrading agents from degraded lands for natural rehabilitation. However, its role on woody species regeneration in the Loma Bosa District of ...

Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species

The banteng ( Bos javanicus ) is an endangered species within the wild Asian Bos complex, that has traditionally been subdivided into three geographically isolated subspecies based on (i) mainland Southeast Asia ( B...

Temporal changes in the Swiss flora: implications for flower-visiting insects

Local floristic diversity has massively decreased during the twentieth century in Central Europe even though in the 1990s diversity began increasing again in several regions. However, little is known whether t...

Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting

Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address con...

Sexual selection leads to positive allometry but not sexual dimorphism in the expression of horn shape in the blue wildebeest, Connochaetes taurinus

Sexual selection is thought to be an important driver of adaptation, speciation and extinction. Empirically testing these predictions across macroevolutionary timescales first requires an understanding of the ...

Genomic patterns of divergence in the early and late steps of speciation of the deep-sea vent thermophilic worms of the genus Alvinella

The transient and fragmented nature of the deep-sea hydrothermal environment made of ridge subduction, plate collision and the emergence of new rifts is currently acting to separate of vent populations, promot...

Large mammal telomere length variation across ecoregions

Telomere length provides a physiological proxy for accumulated stress in animals. While there is a growing consensus over how telomere dynamics and their patterns are linked to life history variation and indiv...

Tick range expansion to higher elevations: does Borrelia burgdorferi sensu lato facilitate the colonisation of marginal habitats?

Parasites can alter host and vector phenotype and thereby affect ecological processes in natural populations. Laboratory studies have suggested that Borrelia burgdorferi sensu lato, the causative agent of human L...

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Effects of warming and isolation from precipitation on the soil carbon, nitrogen, and phosphorus, and their stoichiometries in an alpine meadow in the Qinghai–Tibet Plateau: A greenhouse warming study

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This study quantitatively reviewed the literature related to SDG 11 (Sustainable Development Goal 11) between 2015 and 2022 using bibliometric and spatial autocorrelation methods. The results showed that the amount of SDG 11-related literature increased annually since 2015, with an accelerated growth after 2018. The collaborations among countries, institutions, and authors of SDG 11-related literature were identified, with some major authors and institutions acting as links Keyword cluster and timeline analysis indicated that ‘Agenda 2030’, ‘appropriate technologies’, and ‘country’ were the main clusters of research, while ‘management,’ ‘climate change,’ and ‘impact’ were the most popular keywords, and ‘urban plan nexus,’ ‘social cooperation,’ and ‘renewable energy’ were the emerging keywords since 2021. Spatial autocorrelation analysis revealed that countries with more SDG 11-related literature were dispersed geographically. In the Getis-Ord G* analysis, China, the United States, and the United Kingdom were identified as hotspots; whereas Africa and Central Asia were identified as cold spots. To ensure timely implementation of the SDG 11, this study recommends helping less developed countries, resolving sustainable urbanization issues through innovative technology, and promoting more effective planning. It not only attempts a novel approach of using spatial statistics to analyze the bibliometric results but also provides valuable information for policymakers and scholars.


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Microbial Ecology

In aquatic microbial ecology, a hot-spot is a microenvironment of high microbial abundance, diversity and activities, usually formed from suspended detritus.

From: Encyclopedia of Inland Waters , 2009

Related terms:

N.D. Gray , I.M. Head , in Encyclopedia of Ecology , 2008

Microbial ecology explores the diversity, distribution, and abundance of microorganisms, their specific interactions, and the effect that they have on ecosystems. Although not traditionally thought of as a central discipline within ecology, microbial ecology is of critical importance because microorganisms represent the vast majority of the genetic and metabolic diversity on the planet and drive most of the critical ecosystem processes which recycle matter and energy. Microorganisms have evolved to occupy almost every conceivable ecological niche and energy-generating mechanism. In so doing microorganisms engage in a wide range of ecological interactions with each other and with higher forms of life. Laboratory culture and culture-independent molecular approaches are typically used to identify microbial species, their evolutionary relationships, and the environmental variables that dictate abundance, distribution, and specific activity. Although these approaches are often complementary, they each study microbial ecology from a different perspective. Culture-independent approaches allow the in situ study of microbial interactions and dynamics in complex natural communities. Laboratory cultures have determined the wide metabolic diversity of microorganisms and due to their simplicity and ease of manipulation are invaluable for testing fundamental ecological theories relating to evolutionary adaptation, competition, and demographic tradeoffs.

Microbial ecology

Stephanie A. Yarwood , in Principles and Applications of Soil Microbiology (Third Edition) , 2021

Measurement of microbial diversity and interactions

For many years, soil ecosystem modelers assumed that the quantity of soil microbial biomass was the major driver of decomposition and nutrient cycles, and that substrate availability, temperature, and moisture were the major controlling variables. After discovering the vast diversity and dynamic nature of the soil microbiome, microbiologists began evaluating methods capable of detecting links between changes in community composition and ecosystem functions ( Box 10.4 ). Due to the rapid expansion in microbiological methods, especially nucleic acid-based assays, over the past few decades, it is not possible to cover all available methods in a single chapter. Instead brief descriptions of a select number of these methods follow as examples of approaches for interrogating the soil microbiome.

Soil health

Soils are incredibly diverse in terms of their physical and chemical properties. Soil scientists have long attempted to define soil types in terms that reflect their ability to function in natural and managed settings. The term “soil quality” was coined in this context, but more recently the term “soil health” has become common ( Chapters 14 and 25 14 25 ). Soil quality is the ability of a soil to function within its surroundings, support plant and animal productivity, and maintain or enhance water and air quality. Soil health extends this idea to acknowledge that just as humans function best when they are healthy, so too do soils. Soil microbial communities play an enormous role in soil health; they need to be morphologically and phenotypically diverse enough to successfully occupy the numerous micro-niches found in soil, and to process and partition the wide range of substrate inputs that occur at different times of the year. Several of the critical indicators of soil health include level of organic matter, aggregate stability, water infiltration, crusting, erosion, and acidification. These parameters are strongly influenced directly and/or indirectly by microbial activity. Changes in these soil properties invariably modify the niches occupied by soil microorganisms, resulting in changes in the content, composition, and activities of the microbial community. As part of the effort to define soil health, soil microbiologists have developed procedures to gain insight into community composition and its dynamics at both the taxonomic and functional levels. One important goal is to identify those practices that improve and sustain soil health in agriculture.

Enzymes . The intracellular and extracellular enzymes produced by microorganisms are ultimately responsible for metabolism ( Chapter 3 ). Assays have been developed to measure the potential enzyme activity for processes including denitrification, nitrification, cellulose degradation, and numerous other C, N, and other nutrient transformations ( Burns et al., 2013 ). In the case of denitrification, a soil sample is added to a slurry containing a buffered solution with supplemental C and NO 3 − . The headspace is purged of oxygen and acetylene is added along with N 2 . The acetylene blocks the last step of denitrification resulting in a buildup of N 2 O ( Chapter 15 ). The accumulated N 2 O is then used to calculate the denitrification rate. The activity of enzymes involved in the breakdown of C molecules typically makes use of colorimetric or fluorometric assays, such as the phosphatase assay described in Chapter 19 . In those cases, when the targeted substrate is broken down, a color or light signal is produced. The accumulation of those signals again can be translated into the rate of reaction and potential for conversion of the substrate.

Cellular Fatty Acids. Lipids are essential components of living organisms. Several classes of lipids exist in microorganisms, including phospholipids, glycolipids, lipopolysaccharides, and lipoproteins. Many different fatty acids exist in microbial lipids, and they are used in the identification of microorganisms. In general, soil microbiologists use two relatively straightforward procedures to examine the fatty acid profiles of soils. In one approach, fatty acids are liberated from soil lipids by heating a soil sample at 100°C in a solution of NaOH and methanol. The fatty acids are converted into their methyl ester derivatives (FAME) by heating under hot acidic conditions, whereupon the FAMEs are extracted into an organic solvent such as hexane and analyzed by gas chromatography. Alternately, lipids can be extracted from soil into a mixture of water, chloroform, and methanol, followed by separation of the different classes of lipids (neutral, glycolipids, and phospholipids). Usually, the phospholipid fraction (PLFA) receives the most attention and is analyzed after hydrolysis and methylation under alkaline conditions. The PLFAs are extracted with an organic solvent and analyzed by gas chromatography. Typically, 20–50 fatty acids can be detected and differentiated (more than 100 fatty acids can be identified when more sophisticated extraction and analytical procedures are used). Since some PLFA markers (and other fatty acids) are considered diagnostic for specific microbial groups, these data can help distinguish between microbial communities in different soils, or in a specific soil under different management conditions. This analysis can also be done on a quantitative basis and be used as a measure of microbial biomass. Because both bacteria and fungi contain ester-linked phospholipids, both groups can be simultaneously examined and the relative abundance of select fungal and bacterial PLFAs used to determine the fungal:bacterial ratio. Two drawbacks of common whole-soil lipid-based analyses are (1) they can be used to identify broad groupings such as Gram-positive bacteria and mycorrhiza but have limited taxonomic resolution and cannot distinguish between species and (2) Archaea have ether linkages and are not detected using the same extraction protocol.

DNA Sequencing . New molecular technologies and computing resources have changed many fields within biology, but perhaps none more fundamentally than microbial ecology . The limitations of culturing and microscopy to capture the diversity of the soil microbial community have largely been overcome by increased capacity to sequence millions of stretches of DNA simultaneously. For example, numerous studies have targeted regions of the 16S rRNA genes using PCR ( Chapter 4 ) and then applied bioinformatics to match those sequences against publicly available databases for sequence identification and calculation of diversity metrics.

This is the primary way that researchers currently survey soil microbial community composition across soil types, land management, and disturbance. For example, Williams et al. (2013) sequenced 16S rRNA bacterial genes and used multivariate statistics to visualize differences in community composition in soils that had developed from sand deposits along the coast of Lake Michigan, United States ( Fig. 10.13 ). Further investigation of this data set revealed that bacteria belonging to Acidobacteria increased but Cyanobacteria decreased in abundance with increasing age ( Fig. 10.14 ).

ecology research articles

Figure 10.13 . Multivariate ordinations are a way to distill information from thousands of species so as to visualize differences between microbial community compositions.

In this example, bacterial communities were characterized using 16S rRNA gene sequencing, and each point on the ordination represents the bacterial community at different ages of soil development (chronosequence) in sand deposits along the coast of Lake Michigan, United States.

ecology research articles

Figure 10.14 . Relative abundance of 16S rRNA gene sequences belonging to Acidobacteria (A) and Cyanobacteria (B) at different ages of soil development in sand deposits along the coast of Lake Michigan, United States.

In addition to amplicon sequencing, where PCR is used to create numerous copies of a target gene, researchers may decide to apply shotgun metagenomics. In this case, soil DNA is directly sequenced without the preliminary PCR step. The resulting sequences typically represent 300–900 bp stretches of DNA that can code for any part of the microbial genome. This requires a larger sequencing capacity to sufficiently sample the community and also requires significantly more computing power. The advantage of this approach is the elimination of PCR bias and the potential to sequence yet unknown genes for which PCR primers have not been developed.

RNA Analysis . Although DNA sequencing has been a method of choice for characterizing microbial communities, it has limitations. One of the most significant being that we cannot easily distinguish between DNA from active versus dormant microorganisms. Consider if we went to a meadow to characterize the plant community but could not tell the difference between plants that were growing when we visited and seeds that were in the soil yet to sprout. Understandably, community composition and the amount of DNA in the soil have been found to rarely correlate to function at a specific time point. A more direct measure of activity is the mRNA transcribed when cells are manufacturing the enzymes needed to carry out a particular function. A growing number of studies have targeted mRNA that codes for specific activities such as denitrification ( Chapter 15 ). Compared to DNA-based analyses, far fewer studies have targeted mRNA because it is less stable in the soil, and therefore difficult to extract. However, mRNA-based analyses can provide a more accurate measure of specific microbial activities than DNA-based analyses because mRNA is only transcribed in large quantities when a process is being induced. For example, when soils initially become anaerobic, we may observe increased transcripts associated with denitrification, but those transcripts might be present in lower numbers when the system has been anaerobic for an extended period because the enzymes have already been translated. For example, Theodorakopoulos et al. (2017) examined mRNA transcript abundance in an agricultural field following a rain event. Their goal was to understand what enzymatic processes may contribute to increased N 2 O ( Fig. 10.15 ). Because N 2 O can be generated during nitrification and denitrification, this approach allowed the researchers to identify which pathway was likely contributing the most N 2 O and in what stage of wetting and drying.

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Figure 10.15 . Quantification of gene expression by quantitative PCR for bacterial and archaeal genes involved in nitrification ( amoA ) and denitrification ( nirS , nirK , nosZ ) before and after a rainfall event (gray shading) .

Differences are indicated by (*) when the value was significantly different from those obtained at the two first sampling dates (prior to the rain event).

Stable Isotope Probing . Stable isotopes are useful tools for tracking the fate of molecules through the microbial community and determining which organisms are responsible for specific processes. Biogeochemists use isotopes to determine the rate of processes such as nitrogen mineralization ( Chapter 15 ). More recently these tracers have been added to soils as a way to label the microbial community, in a method known as stable isotope probing (SIP). For example, 13 C-labeled cellulose can be added to soil, and the 13 C allowed to be incorporated into the microbial biomass during metabolism. This approach is based on the principle that organisms which catabolize the cellulose will incorporate a portion of the 13 C into their cells. The label can then be detected in cellular lipids and nucleic acids to determine which organisms are catalyzing the process of interest. In the case of DNA- and RNA-SIP, the labeled and unlabeled nucleic acids are separated using ultracentrifugation ( 13 C being heavier than 12 C) and the different fractions then analyzed by sequencing or another approach.

Emerging Technologies . Numerous microbial characterization methods have been developed over the last 2 decades that take advantage of the molecules produced by soil microorganisms. Methods development for metaproteomics is on-going but would allow us to describe all of the proteins (including enzymes) in the soil in a manner similar to DNA-based metagenomics. Another approach is metabolomics where microbial metabolites including amino acids, sugars, and alcohols are extracted and described. Each approach has advantages and disadvantages when it comes to methodological constraints and interpretability.

Due to the complexity of the microbial community, a multi-pronged approach likely yields the most accurate information. For example, Mbuthia et al. (2015) compared microbial community composition, activity, and soil quality in response to differences in farming systems that included tillage versus no-till practices and the presence of cover crops. They concluded that long-term differences in farming practices altered the microbial community and its function, with most analytical methods indicating benefits (e.g., increased microbial activity and biomass) from use of no-till practices and/or cover crops. However, treatment benefits varied depending on the parameter being measured. For example, a vetch cover crop produced higher β-glucosaminidase and basal microbial respiration rates but lower mycorrhizal biomass levels compared to wheat and no cover crop.

Another study examined the effects of drought and rainfall on the soil microbial communities in native tall grass prairies ( Roy Chowdhury et al., 2019 ). Soil samples were collected and subjected to either wetting or drying. mRNA sequencing was used to determine how bacteria responded to these potential stressors, by identifying the decrease or increase of gene expression ( Fig. 10.16 A). Additionally, metabolomics was used to examine the change in metabolites following moisture shifts ( Fig. 10.16 B). Along with DNA sequencing, these data were compiled to create reaction-metabolite integrative bipartite networks, in other words, metabolic maps of how soils react to wetting and drying ( Fig. 10.16 C). This basic information about how the soil microbiome changes during wetting and drying can help us understand the short- and long-term effects of climate change on soil functioning and health.

ecology research articles

Figure 10.16 . Multi-omics characterization of soil microbiome response to wetting and drying.

(A) Metatranscriptome data with heat map showing the top 20 most abundant transcripts (enzyme name listed) observed under dry compared to wet conditions. The x -axis indicates soil sample (1 or 3) and treatment (W, wet; D, dry). Moisture conditions are also indicated by the header row in blue (wet) or red (dry). The color gradient for each cell is scaled to a log 2 fold change of −2 to 2. (B) Bar charts showing the metabolome (relative abundance of selected metabolites) from three native prairie soils (1, 2, and 3) ( gray , control; blue , wet; red , dry). (C) Metabolite networks for soil 1. Colored symbols indicate reactions that are more prevalent under specific incubation conditions: blue , wet; red , dry; yellow , both. Yellow shading highlights specific pathways that are more prevalent under dry conditions. Larger nodes represent the commonly predicted reactions in both soils (1 and 3), while small nodes represent the uniquely predicted reactions.

Summation of the Microbial Ecology of Biochar Application

C.H. Orr , T. Komang Ralebitso-Senior , in Biochar Application , 2016

Microbial ecology analysis is a relatively new topic within the emergent biochar research field. As a consequence, each of the book chapters presented a discourse on knowledge development progress with regards to biochar impacts on soil micro- and macrobiological communities in a wide range of ecosystems and contexts. The method potentials, knowledge gaps, and future investigations required to address these, for research and application purposes, were highlighted specifically. Therefore this chapter considers key in-book discussions to develop a précis of the future research opportunities and applications of (molecular) microbial ecology methods in biochar-augmented or -impacted ecosystems. Also parallel to the need to address research and application questions by the newest approaches are reflections on biochar-directed policy where guidelines are required to underpin biochar research while investigative findings must, in turn, inform policy development.

Knowledge Gaps, Obstacles, and Research Frontiers in Groundwater Microbial Ecology

Christian Griebler , ... Grant C. Hose , in Reference Module in Earth Systems and Environmental Sciences , 2022


Microbial ecology is a rapidly evolving discipline, perhaps more than other branches of ecology, as new technologies and declining costs are transforming our ability to characterize communities and identify and quantify their functions. While the discipline moves forward, there remain a suite of key research questions that are specific to groundwater ecosystems that require urgent further research. The often stable and simplified groundwater environment provides a unique test bed for experimentation and observation, and provides opportunities for progressing deep-seated ecological theories.

Addressing the questions discussed here will undoubtedly progress understanding of microbial and groundwater ecology, but will also have immense social and economic benefits given the importance of groundwater microbes to water quality and the delivery of ecosystem services on which the majority of earth‘s population relies.

Metagenomic approaches to study the culture-independent bacterial diversity of a polluted environment—a case study on north-eastern coast of Bay of Bengal, India

Jaya Chakraborty , ... Surajit Das , in Microbial Biodegradation and Bioremediation (Second Edition) , 2022

5.6 Conclusion

Microbial ecology effectively assesses the total microbial diversity, particularly about detecting uncultivable and fastidious microbial species and those exist in low abundance. Metagenomics has paved the way for microbiologists to deal with the uncultivable microbes, redefining the concept of a genome, and accelerated the rate of gene discovery. Metagenomics mediated taxonomic and functional analysis have identified novel microbes, new enzymes, antibiotics having potential applications in biotechnology and medicine. The marine environment with vast diversity and complexity is the most threatened ecosystem of the globe. The Bay of Bengal on India’s east coast is a point for national and international trade having well-known ports, such as Paradip Port and Visakhapatnam Port. Exploring these marine environments unlocks the classification of novel microbes that can be employed for bioremediation of toxic chemicals and environmental toxicants. The present case study collectively provided the assessment of total unculturable bacterial diversity from the various sediment samples of the coastal marine environments. From the metagenome sequences, the highest bacterial diversity with total OTUs of 18,662 and Shannon diversity index of 10.03 was observed at sample S2 (Paradip Port) by Illumina sequencing of the hypervariable V3–V4 region of 16S rRNA gene. Amplicon sequencing and QIIME analysis of the metagenomic samples indicated huge marine microbial diversity, which can be harnessed further for several biotechnological applications. At the phylum level, the samples were enriched with Proteobacteria , indicating the anthropogenic pressure on these marine habitats. Genus of Corynebacterium , Pseudomonas , and Anaerococcus were abundant in these regions. Thus the present study has documented the abundant genera of uncultivable marine bacteria from the east coast of the Bay of Bengal. However, extensive research is required in metagenomics in the light of biochemistry, taxonomy, and genetics to culture, identity, and completely exploit these microorganisms for various biotechnological applications. The development of multi-omics approaches will be a highly demanding area of research in the coming years. Metagenome-sequencing assisted with metatranscriptomics and metabolomics will provide the complete snapshot of biodiversity, functional attributes, and metabolic potential from a diverse environment, which will save a huge budget and time.

Microbiomes and Holobionts

Derek Skillings , Katarzyna Hooks , in Encyclopedia of Ecology (Second Edition) , 2019

Microbial ecology aims to determine the patterns and drivers of microbial community distribution, interaction, and assembly. It has been well demonstrated that microbial community composition changes across most environmental gradients, such as geographic distance, nutrients, temperature, moisture levels, salinity, oxygen availability, pH, and day length. Broader patterns have been difficult to track because of the necessarily small-scale of individual studies. Initiatives like the Earth Microbiome Project bring together regional studies that tend to focus on one type of environmental sample in one locality in order to investigate microbial community dynamics at larger regional and global scales. Environmental microbiome samples from diverse environments are paired with metadata consisting of spatial, temporal, physiochemical, and animal/plant association variables. Initial studies looked at covariation between microbial diversity, measured in terms of operational taxonomic units (OTUs) clustered by single-gene sequencing (usually 16S rRNA), and environmental variables. These approaches have expanded to take advantage of whole-genome methods, strain-level diversity, and more fine-grained sampling. Initial results show a general pattern of hierarchical organization, with less-rich communities nested within richer communities at higher taxonomic levels.

Wastewater Treatment and Reuse

I.L.C. Drexler , ... D. Yeh , in Comprehensive Water Quality and Purification , 2014 Biological Characteristics

Treatment efficiency can be affected by biological characteristics, such as microbial ecology or antibiotics, or estimated by using biomarkers and indicator organisms. Other constituents, such as pathogens, may influence the ability of wastewater products to be recovered and reused. Microbial ecology

The microbial ecology , or species distribution of the microscopic community, of wastewater will vary depending on the environmental conditions, a function of wastewater source or stage in the treatment process. Microbial ecology can be used to judge the efficiency of the biological processes; stalked ciliates in the activated sludge demonstrate healthy sludge age and reliable organics removal. If microbial ecology is dominated by pathogens, treatment efforts must be focused on disinfection before safe resource recovery can be guaranteed. Pathogens

Pathogens in wastewater can include bacteria, protozoa, helminths, viruses, or prions (for a thorough review of individual organisms see Madigan and Martinko (2005) ). Table 4 lists the typical pathogens and their concentration in raw and treated wastewater. It should be noted that the presence of pathogens in wastewater will be a function of the epidemiological health of a community; a higher infection rate in the community will cause higher pathogen concentrations in that community's wastewater.

Table 4 . Pathogenic organisms potentially present in raw and treated wastewater

Pathogenic organisms are typically killed in wastewater or biosolids through disinfection processes such as chlorination, ultraviolet (UV), or heat exposure. To safely reuse wastewater effluent or biosolids, it is imperative that pathogenic materials are adequately eliminated such that public and environmental health is not compromised for the sake of water and energy conservation. Indicator organisms and biological signatures

Biomarkers are biologically derived constituents in wastewater that can point to treatment efficiency, wastewater origin, or community lifestyles. If present after treatment, indicator organisms such as coliform bacteria imply that other pathogenic bacteria have also survived the disinfection process, thereby rendering the treated water unsafe for reuse. Similarly, bacteria, viruses, or phages can be used to trace the origin of wastewater ( Rosario et al., 2009; Weidhaas et al., 2010; Mcquaig et al., 2006; Brownell et al., 2007 ). Other biomarkers, such as pharmaceuticals, caffeine, sucralose, or menthol can be used to assess the overall health, diet, or lifestyle of a community. These biomarkers have been used in Europe, North America, and Australia to study public and environmental health of specific communities ( Thomas and Reid, 2011; Soh et al., 2011; van Nujis et al., 2010 ). Antibiotics

Antibiotics enter wastewater through human excrement, flushing of excess pills, landfill leachate, or agricultural, veterinary, or hospital waste and have the ability to influence or disrupt biological processes in wastewater treatment. Some antibiotics may attack activated sludge and nitrifying bacteria ( Kim and Aga, 2007b ), reducing treatment efficiency. Wastewater treatment plant design and operation may influence effluent residual antibiotics and antibiotic-resistant bacteria ( Kim and Aga, 2007b ), but wastewater treatment itself may positively select for resistant bacteria ( Ferriera Da Silva et al., 2006 ). Increased presence of antibiotics in the environment can reduce their efficacy by encouraging bacteria to develop antibiotic-resistant genes, which has helped almost every bacterial pathogen to be resistant to at least one clinical antibiotic ( Munir et al., 2011 ). Table 5 lists the selected antibiotics found in wastewater before and after treatment (for more extensive data, see Kim and Aga (2007b) , Ferriera Da Silva et al. (2006) , Munir et al. (2011) , and Zhang and Li (2011) .

Table 5 . Antibiotics and antibiotic-resistant genes and bacteria found in wastewater

Abbreviations: AML, amoxicillin; AS, activated sludge; CIP, ciprofloxacin; Cl, chlorination disinfection; ERY, erythromycin; GEN, gentamicin; MBR, membrane bioreactor; MF/RO, microfiltration/reverse osmosis; ND, not detected; NT, not treated; OD, oxidative ditch; PT, primary treatment; RBC, rotary biological contactors; Sul , sulfonamide-resistant gene; TET, tetracycline; Tet , tetracycline-resistant gene; UN, unspecified; and UV, ultraviolet radiation disinfection.

Stream Microbial Ecology in a Changing Environment

S. Findlay , in Stream Ecosystems in a Changing Environment , 2016

Understanding of SME will undoubtedly advance rapidly in the coming decades in large part due to increased capacity to collect data about microbes and the processes they catalog, but also because the likely rapid changes in microbial composition and function will invigorate the research community. The measurement tools and conceptual frameworks have and will continue to improve, but we may be tracking a much faster moving target than ever before. I believe the methodological improvements will keep pace and so it becomes our responsibility to develop, adopt, and reject ideas about which factors are important, which factors interact, and how the huge microbial plasticity might respond to streams in a (rapidly) changing environment.

Biochar Effects on Ecosystems

E.-L. Ng , T.R. Cavagnaro , in Biochar Application , 2016

To reflect the microbial ecology techniques being applied currently, this chapter aims to explore how the phospholipid fatty acids can be used to determine how biochar affects the structural, compositional, and functional capacities of microbial communities in different soil ecosystems. Used in combination with natural isotope or radioisotope ( 13 C or 14 C)-labeled substrates, it has the potential to determine soil organic matter cycling rate, monitor C flows from plants to soil microbes, and identify below-ground trophic relationships. Insights into biochar effects on soil phospholipid fatty acids, alternatives to data analysis, its limitations, and knowledge gaps are highlighted.

Climate, Geography, and Soil Abiotic Properties as Modulators of Soil Carbon Storage

Manuel Delgado-Baquerizo , ... Brajesh K. Singh , in Soil Carbon Storage , 2018

5.5.1 Microbial Ecology

The role of microbial ecology in predicting soil C stocks is addressed with detail in Chapter 3 , Microbial Modulators and Mechanisms of Soil Carbon Storage. Studies suggest that inclusion of soil microbial-derived information, including microbial biomass ( Wieder et al., 2013 ) and microbially-driven processes (enzyme activities and nutrient cycling; Allison et al., 2010 ; Trivedi et al., 2016 ) can improve the prediction of soil C stocks at regional and global scales. These models included microbial communities using a “Black-Box” approach ( Schimel and Schaeffer, 2012 )—i.e., we do not know who is in there, but their activity relates to soil C stocks. Much less is known however, on whether the inclusion of omics-derived information on microbial community composition, structure (fungi-to-bacteria ratio) and functional profiles might also help explain unique portions of the variations in soil C stocks. The abundance of functional genes has recently been demonstrated to be strongly linked to soil C concentrations and functions ( Trivedi et al., 2016 ), suggesting that this information may lead to improvements in the predictions of soil C stocks. In addition, microbial community composition per se may also explain a unique portion of the variation of soil C via the information provided by particular microbial life-strategists. For example, oligotrophic groups such as Actinobacteria, Acidobacteria and Deltaproteobacteria ( Fierer et al., 2007; Bastian et al., 2009 ; Trivedi et al., 2013 ) are expected to promote low respiration rates and to prefer soils with low levels of carbon where they are more competitive. On the contrary, copiotrophic organisms such as Gamma-proteobacteria, Alpha-proteobacteria and Bacteroidetes ( Fierer et al., 2007 ; Trivedi et al., 2013 ) seem to prefer environments that are rich in carbon and often promote labile carbon decomposition and high respiration rates in soil. This information can be used to target particular groups of microorganisms—microbial indicators of soil C—to improve predictions of C stocks under future scenarios. The use of this type of data is especially timely as recent studies have provided evidence that (1) major phyla/classes are globally distributed and common across samples (e.g., Ramirez et al., 2012 ), and (2) the use of high bacterial taxonomic ranks (phyla and classes) is strongly linked to ecosystem functioning ( Philippot et al., 2010 ; Trivedi et al., 2013 ). In addition to dominant microbial taxa, soil bacteria, and fungi are well-known to have different capacities to decompose organic matter, to perform soil respiration and to incorporate C into the soil ( Philippot et al., 2010 ; Trivedi et al., 2013 ). Because of this, incorporating both information from bacteria and fungi, as well as from their relative abundance (fungi-to-bacteria ratio), may further improve the prediction of soil C stocks. “Next generation” studies on C modeling will need to assess the utility of this data and to identify the most valuable—from an economic and practicality point of view—microbial predictors of soil C stocks.

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