scholarly journals Ocean viruses and their effects on microbial communities and biogeochemical cycles

10.3410/b4-17 ◽  
2012 ◽  
Vol 4 ◽  
Author(s):  
Joshua S. Weitz ◽  
Steven W. Wilhelm
Keyword(s):  
Microbial Communities ◽  
Biogeochemical Cycles

scholarly journals Insights into the Variations of Hao-Dependent Nitrifying and Nir-Dependent Denitrifying Microbial Communities in Ammonium-Graduated Lake Environments

2019 ◽  
Vol 9 (16) ◽  
pp. 3229
Author(s):  
Zhao ◽  
Chen ◽  
Qu ◽  
Jin ◽  
Zheng ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Spatial Scales ◽  
Biogeochemical Cycles ◽  
Nitrifying Bacteria ◽  
Microbial Populations ◽  
High Nitrogen ◽  
Hydroxylamine Oxidoreductase ◽  
Nitrosomonas Oligotropha

Biological nitrification and denitrification play significant roles in nitrogen-associated biogeochemical cycles. However, our understanding of the spatial scales at which microbial communities act and vary is limited. We used gene-specific metagenomic PCR to explore changes in nitrifying and denitrifying microbial communities within pristine lake and its branches, where the ammonium and dissolved organic carbon (DOC) concentrations form a gradient. The biomarkers hydroxylamine oxidoreductase and nitrite reductase genes indicated that strong relationships exist between the diversities and community structures of denitrifiers and ammonium gradients. It showed that the Nitrosomonas oligotropha cluster dominates the nitrifying bacteria in low-nutrition environments, while a new Nitrosomonas ureae cluster accounted for nearly 80% of the nitrifying bacteria in high-nitrogen environments. The distribution and diversity of nirS/K-dependent denitrifiers in the various habitats were similar, but predominantly affiliated with unknown clusters. Moreover, the abundance of all the hao genes dramatically outnumbered that of nir genes. The relative abundance of hao was clearly higher during eutrophication (13.60%) than during oligotrophy (5.23%), whereas that of nirS showed opposite tendencies. Overall, this study provides valuable comparative insights into the shifts in nitrifying and denitrifying microbial populations in lake environments with ammonium gradients, suggesting that unique dominant denitrifiers probably play an important role in the nitrogen cycle.

scholarly journals Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil

2019 ◽  
Vol 7 (5) ◽  
pp. 129 ◽  
Author(s):  
Dong Liu ◽  
Katharina M. Keiblinger ◽  
Sonja Leitner ◽  
Uwe Wegner ◽  
Michael Zimmermann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Global Climate ◽  
Soil Microbial Communities ◽  
Biogeochemical Cycles ◽  
Functional Responses ◽  
Soil Microbial ◽  
Metabolic Functions ◽  
Drying And Rewetting ◽  
Different Levels ◽  
Simultaneous Variation

Global climate change is predicted to alter drought–precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought and following rewetting events, using a soil metaproteomics approach. For this, an established field experiment located in an Austrian forest with two levels (moderate and severe stress) of precipitation manipulation was evaluated. The results showed that fungi were more strongly influenced by drying and rewetting (DRW) than bacteria, and that there was a drastic shift in the fungal community towards a more Ascomycota-dominated community. In terms of functional responses, a larger number of proteins and a higher functional diversity were observed in both moderate and severe DRW treatments compared to the control. Furthermore, in both DRW treatments a rise in proteins assigned to “translation, ribosomal structure, and biogenesis” and “protein synthesis” suggests a boost in microbial cell growth after rewetting. We also found that the changes within intracellular functions were associated to specific phyla, indicating that responses of microbial communities to DRW primarily shifted microbial functions. Microbial communities seem to respond to different levels of DRW stress by changing their functional potential, which may feed back to biogeochemical cycles.

scholarly journals Extracellular ribosomal RNA provides a window into taxon-specific microbial lysis

2021 ◽  
Author(s):  
Kevin Xu Zhong ◽  
Amy M Chan ◽  
Jennifer F Wirth ◽  
Curtis A Suttle
Keyword(s):  
Microbial Communities ◽  
Ribosomal Rna ◽  
Biogeochemical Cycles ◽  
Specific Cell ◽  
Sequence Variants ◽  
Viral Lysis ◽  
Functional Roles ◽  
Proposed Model ◽  
Life On Earth ◽  
Marine Microbial Communities

Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here we determined taxon-specific cell lysis of prokaryotes in coastal seawater by sequencing extracellular and cellular ribosomal RNA (rRNA). We detected lysis in about 15% of the 16946 prokaryotic amplicon sequence variants (ASVs) identified, and lysis of up to 34% of the ASVs within a water sample. High lysis was most commonly associated with rare but typically highly productive bacteria, while relatively low lysis was more common in taxa that are often abundant, consistent with the proposed model of "kill the winner", and the idea that less abundant taxa generally experience higher relative lysis than dominant taxa. These results provide an explanation to the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance.

scholarly journals Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

2013 ◽  
Vol 79 (13) ◽  
pp. 4031-4040 ◽  
Author(s):  
Loïc Nazaries ◽  
Yao Pan ◽  
Levente Bodrossy ◽  
Elizabeth M. Baggs ◽  
Peter Millard ◽  
...  
Keyword(s):  
Land Use ◽  
Land Use Change ◽  
Microbial Communities ◽  
Climate Models ◽  
Methane Flux ◽  
Biogeochemical Cycles ◽  
Stable Isotope Probing ◽  
Community Diversity ◽  
Ecosystem Functions ◽  
Atmospheric Methane

ABSTRACTMicrobes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.

scholarly journals Spatial Variability of Abyssal Nitrifying Microbes in the North-Eastern Clarion-Clipperton Zone

2021 ◽  
Vol 8 ◽  
Author(s):  
Anita L. Hollingsworth ◽  
Daniel O. B. Jones ◽  
C. Robert Young
Keyword(s):  
Organic Carbon ◽  
Spatial Variability ◽  
Microbial Communities ◽  
Microbial Community Composition ◽  
Biogeochemical Cycles ◽  
Rrna Gene ◽  
Seafloor Topography ◽  
Ammonia Oxidizing Archaea ◽  
The North ◽  
Polymetallic Nodules

Abyssal microbes drive biogeochemical cycles, regulate fluxes of energy and contribute to organic carbon production and remineralization. Therefore, characterizing the spatial variability of benthic microbes is important for understanding their roles in benthic environments and for conducting baseline assessments of areas of the seabed that might be targeted by commercial mining activities. Yet, detailed assessments of the spatial distributions of benthic microbial communities in these regions are still incomplete, and these efforts have not yet considered the influence of seafloor topography and heterogeneity on microbial distributions across a range of scales. In this study, we investigated the composition and spatial variability of benthic microbial assemblages found in sediments and polymetallic nodules collected from the Clarion Clipperton Zone (CCZ) in the equatorial Pacific (4000–4300 m water depth). We used 16S rRNA gene sequences to characterize these communities. The upper 20 cm of abyssal sediments harbored diverse and distinctive microbial communities in both sediments and their associated polymetallic nodules, with high similarity across topographical areas of the seabed. Assemblage composition differed vertically through the sediment, by habitat and across small to mesoscales. Potential carbon-fixing microbes formed more than 25% relative abundance of sediment assemblages, which were dominated by ammonia-oxidizing Archaea Nitrosopumilus. Non-photosynthetic Cyanobacteria were more frequent in the deeper sediment layers and nodules. Sediment communities had a higher abundance of taxa involved in nitrogen cycling, such as Nitrosopumilus, Nitrospina, Nitrospira, AqS1 (Nitrosococcaceae), and methanogens wb1-A12 (NC10 phylum). In contrast, nodules were more enriched in Alphaproteobacteria, Gammaproteobacteria, Planctomycetes, Acidobacteria, Bacteroidetes, Nanoarchaeaeota, and Calditrichaeota. Microbes related to potential metal-cycling (Magnetospiraceae and Kiloniellaceae), organic carbon remineralization (Woeseia), and sulfur-oxidizing Thiohalorhabdaceae were also more enriched in nodules. Our results indicate that benthic microbial community composition is driven by sediment profile depth and seafloor heterogeneity at small and mesoscales. The most abundant microbial taxa within the sediments were nitrifying and putative carbon-fixing microbes, and may have key ecological roles in mediating biogeochemical cycles in this habitat.

scholarly journals Monitoring a changing Arctic: Recent advancements in the study of sea ice microbial communities

AMBIO ◽  
2021 ◽  
Author(s):  
Karley Campbell ◽  
Ilkka Matero ◽  
Christopher Bellas ◽  
Thomas Turpin-Jelfs ◽  
Philipp Anhaus ◽  
...  
Keyword(s):  
Sea Ice ◽  
Microbial Communities ◽  
Marine Ecosystem ◽  
Sustainable Use ◽  
Biogeochemical Cycles ◽  
The Arctic ◽  
Human Consumption ◽  
Microbial Life ◽  
New Methodologies ◽  
Healthy Functioning

AbstractSea ice continues to decline across many regions of the Arctic, with remaining ice becoming increasingly younger and more dynamic. These changes alter the habitats of microbial life that live within the sea ice, which support healthy functioning of the marine ecosystem and provision of resources for human-consumption, in addition to influencing biogeochemical cycles (e.g. air–sea CO2 exchange). With the susceptibility of sea ice ecosystems to climate change, there is a pressing need to fill knowledge gaps surrounding sea ice habitats and their microbial communities. Of fundamental importance to this goal is the development of new methodologies that permit effective study of them. Based on outcomes from the DiatomARCTIC project, this paper integrates existing knowledge with case studies to provide insight on how to best document sea ice microbial communities, which contributes to the sustainable use and protection of Arctic marine and coastal ecosystems in a time of environmental change.

scholarly journals Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Huajun Zhang ◽  
Kai Wang ◽  
Lixin Shen ◽  
Heping Chen ◽  
Fanrong Hou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Nitrogen Metabolism ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Biogeochemical Cycles ◽  
Early Spring ◽  
Diatom Bloom ◽  
Ecological Processes ◽  
Content Type

ABSTRACTHarmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes.Rhodobacteraceae,Flavobacteriaceae, andMicrobacteriaceaewere the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyllacontents, which were affected mainly bySkeletonema costatum. Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCEHarmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

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