4.8 Article

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments

Related references

Note: Only part of the references are listed.
Article Geochemistry & Geophysics

Analysing seasonal variations of methane oxidation processes coupled with denitrification in a stratified lake using stable isotopes and numerical modeling

Gisela Alejandra Pena Sanchez et al.

Summary: This study investigates methane oxidation processes in the water column of a seasonally stratified lake and quantitatively describes the contribution of anaerobic and aerobic methane oxidation in removing methane from the water column throughout the year. The results show that anaerobic methane oxidation coupled with denitrification is the dominant methane sink in the lake during summer stratification, and its location within the water column varies with the seasonal vertical displacement and availability of nitrate.

GEOCHIMICA ET COSMOCHIMICA ACTA (2022)

Article Ecology

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

Ya-Jou Chen et al.

Summary: This study investigated the relationships between microbial community composition and biogeochemical processes in coastal sediments exposed to varying levels of hydrodynamic disturbance. The findings suggest that hydrodynamic disturbance plays a critical role in controlling microbial community assembly and biogeochemical processes in coastal sediments. The study provides insights into the mechanisms underlying the interactions between microbial communities and biogeochemical dynamics in these unique environments.

ISME JOURNAL (2022)

Review Microbiology

Priority effects in microbiome assembly

Reena Debray et al.

Summary: The order and timing of microbial arrival can significantly impact microbiome composition and function, with studies highlighting the importance of priority effects in different environments. Detection methods and mechanisms of priority effects are discussed in this review.

NATURE REVIEWS MICROBIOLOGY (2022)

Article Engineering, Environmental

Nitrogen recovery through fermentative dissimilatory nitrate reduction to ammonium (DNRA): Carbon source comparison and metabolic pathway

Yiyi Zhao et al.

Summary: This study constructed three organic substances supported DNRA systems in a membrane bioreactor and investigated the effect of different COD/N ratios on ammonium nitrogen transformation efficiency and microbial community diversity. The results showed that the ethanol-supported DNRA system at a COD/N ratio of 7.7 had the highest ammonium nitrogen transformation efficiency and nrfA gene abundance, and contained a large number of fermenting bacteria. In addition, potential metabolic pathways of three carbon sources were predicted.

CHEMICAL ENGINEERING JOURNAL (2022)

Article Multidisciplinary Sciences

Emergent phases of ecological diversity and dynamics mapped in microcosms

Jiliang Hu et al.

Summary: Using bacterial microcosms, researchers found predictable emergent patterns of diversity and dynamics in ecological communities, showing that high biodiversity and fluctuations reinforce each other.

SCIENCE (2022)

Article Geosciences, Multidisciplinary

GeoDAR: georeferenced global dams and reservoirs dataset for bridging attributes and geolocations

Jida Wang et al.

Summary: Dams and reservoirs are widespread human-made infrastructures, but there is a lack of comprehensive spatial inventories for them. Existing datasets either focus on dam quantity and spatial coverage or detailed attributes for limited dams. To bridge this gap, researchers have introduced a new dataset, GeoDAR, which provides spatially explicit information for dams and reservoirs worldwide. This dataset is expected to have significant implications for hydrologic modeling, water resource management, ecosystem health, and energy planning.

EARTH SYSTEM SCIENCE DATA (2022)

Review Microbiology

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Anna J. Wallenius et al.

Summary: Large amounts of methane are produced by methanogenic archaea in anoxic sediments, with over 90% of it being oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ). Coastal systems contribute to the majority of total marine methane emissions, and factors like eutrophication and climate change can influence methane emissions from these systems. Further studies are needed to understand the processes and microorganisms involved in methane cycling and to predict methane emissions accurately from coastal zones in the future.

FRONTIERS IN MICROBIOLOGY (2021)

Article Ecology

Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem

Ya-Jou Chen et al.

Summary: This study found that habitat generalists tend to dominate in highly dynamic environments, while habitat specialists are restricted to narrower niches in permeable sediments. The ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms, with broad ecological and biogeochemical implications.

ISME JOURNAL (2021)

Article Limnology

The impact of seasonal sulfate-methane transition zones on methane cycling in a sulfate-enriched freshwater environment

Jan F. Kleint et al.

Summary: Lake Willersinnweiher in Germany releases methane to the atmosphere continuously throughout the year, with intense anaerobic oxidation of methane in sediment layers. The interaction between carbon and sulfur cycling affects methane release and consumption processes in the lake. Aerobic oxidation processes in the water column act as a barrier to minimize methane release into the surface water and atmosphere.

LIMNOLOGY AND OCEANOGRAPHY (2021)

Article Environmental Sciences

The Investigation of the Connections Among Hydrogeological Factors and the Emissions of Two Greenhouse Gases in Lake Sediment

Xiang Lu et al.

Summary: This study investigated the correlations between water content and microbial gas emissions in layered sediment from Chaohu Lake. Results showed that microbial methane emissions influence sediment structure and water content, while carbon dioxide emissions may be related to water content in different layers. The research also discussed the significance of methane emissions in material exchange between water and sediment, providing meaningful information for studying environmental factors and microbial ecology relationships.

WATER RESOURCES RESEARCH (2021)

Article Ecology

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Clemens Schauberger et al.

Summary: The study found that microbial communities in Hadal trenches exhibit high similarity within each trench axis and are strongly influenced by sediment depth and redox stratification. Differences in community composition are more related to sediment depth within each trench rather than between different trenches, and not solely explained by total organic carbon content.

ISME JOURNAL (2021)

Article Biology

Dormancy dampens the microbial distance-decay relationship

K. J. Locey et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

Review Environmental Sciences

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial

C. B. Pandey et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2020)

Article Multidisciplinary Sciences

Geochemical transition zone powering microbial growth in subsurface sediments

Rui Zhao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Review Environmental Sciences

River dam impacts on biogeochemical cycling

Taylor Maavara et al.

NATURE REVIEWS EARTH & ENVIRONMENT (2020)

Review Multidisciplinary Sciences

Subseafloor life and its biogeochemical impacts

Steven D'Hondt et al.

NATURE COMMUNICATIONS (2019)

Review Microbiology

Ecology and evolution of seafloor and subseafloor microbial communities

William D. Orsi

NATURE REVIEWS MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Growth of sedimentary Bathyarchaeota on lignin as an energy source

Tiantian Yu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Review Microbiology

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

Zhichao Zhou et al.

FEMS MICROBIOLOGY REVIEWS (2018)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Multidisciplinary Sciences

Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment

Xihan Chen et al.

SCIENTIFIC REPORTS (2017)

Article Microbiology

Fermentative Bacteria Influence the Competition between Denitrifiers and DNRA Bacteria

Eveline M. van den Berg et al.

FRONTIERS IN MICROBIOLOGY (2017)

Review Ecology

Microbial community assembly in marine sediments

Caitlin Petro et al.

AQUATIC MICROBIAL ECOLOGY (2017)

Article Biotechnology & Applied Microbiology

Depth Distribution and Assembly of Sulfate-Reducing Microbial Communities in Marine Sediments of Aarhus Bay

Lara M. Jochum et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2017)

Review Biochemistry & Molecular Biology

Methyl-accepting chemotaxis proteins: a core sensing element in prokaryotes and archaea

Abu Iftiaf Md Salah Ud-Din et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2017)

Article Geochemistry & Geophysics

Controls on subsurface methane fluxes and shallow gas formation in Baltic Sea sediment (Aarhus Bay, Denmark)

Sabine Flury et al.

GEOCHIMICA ET COSMOCHIMICA ACTA (2016)

Article Ecology

NC10 bacteria in marine oxygen minimum zones

Cory C. Padilla et al.

ISME JOURNAL (2016)

Article Multidisciplinary Sciences

Decoupling function and taxonomy in the global ocean microbiome

Stilianos Louca et al.

SCIENCE (2016)

Review Ecology

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

Tadashi Fukami

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 46 (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Geochemistry & Geophysics

Nitrate-dependent anaerobic methane oxidation in a freshwater sediment

Katrin A Nordi et al.

GEOCHIMICA ET COSMOCHIMICA ACTA (2014)

Article Multidisciplinary Sciences

Evidence for nitrite-dependent anaerobic methane oxidation as a previously overlooked microbial methane sink in wetlands

Bao-lan Hu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake

Joerg S. Deutzmann et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biotechnology & Applied Microbiology

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

Dong-Lei Sun et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Morgan G. I. Langille et al.

NATURE BIOTECHNOLOGY (2013)

Article Microbiology

Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal

Vitaly V. Kadnikov et al.

FEMS MICROBIOLOGY ECOLOGY (2012)

Article Multidisciplinary Sciences

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Bente Aa Lomstein et al.

NATURE (2012)

Article Ecology

betapart: an R package for the study of beta diversity

Andres Baselga et al.

METHODS IN ECOLOGY AND EVOLUTION (2012)

Article Chemistry, Analytical

A 100 year sedimentary record of heavy metal pollution in a shallow eutrophic lake, Lake Chaohu, China

Fengyu Zan et al.

JOURNAL OF ENVIRONMENTAL MONITORING (2011)

Article Biochemical Research Methods

Picante: R tools for integrating phylogenies and ecology

Steven W. Kembel et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Ab initio gene identification in metagenomic sequences

Wenhan Zhu et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biotechnology & Applied Microbiology

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum

Katharina F. Ettwig et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)

Article Microbiology

Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea

Katharina F. Ettwig et al.

ENVIRONMENTAL MICROBIOLOGY (2008)

Article Multidisciplinary Sciences

Impact of artificial reservoir water impoundment on global sea level

B. F. Chao et al.

SCIENCE (2008)

Article Multidisciplinary Sciences

A microbial consortium couples anaerobic methane oxidation to denitrification

AA Raghoebarsing et al.

NATURE (2006)

Review Microbiology

Winogradsky and modern microbiology

G. A. Zavarzin

MICROBIOLOGY (2006)

Article Computer Science, Interdisciplinary Applications

PLS path modeling

M Tenenhaus et al.

COMPUTATIONAL STATISTICS & DATA ANALYSIS (2005)

Article Biology

Self-organized instability in complex ecosystems

RV Solé et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2002)

Article Biochemistry & Molecular Biology

Ammonia fermentation, a novel anoxic metabolism of nitrate by fungi

ZM Zhou et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2002)