Organic Carbon and Eukaryotic Predation Synergistically Change Resistance and Resilience of Aquatic Microbial Communities

2021 ◽  
Author(s):  
Wenwen Fang ◽  
Xiaokun Liu ◽  
Xing Mu ◽  
Jiangjian Shi ◽  
Zhiwei Liang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Anthropogenic Activities ◽  
Change Resistance ◽  
Urban Rivers ◽  
Aquatic Microbial Ecology ◽  
Study Laboratory ◽  
Stability Results

Abstract With dramatic global rise of urbanization, anthropogenic activities alter aquatic ecosystems in urban rivers through inputs of dissolved organic carbon (DOC) and nutrients. Microorganisms play crucial roles in global biogeochemical element cycles, providing functions to sustain microbial ecology stability. The DOC (bottom-up control) and microbial predation (top-down control) may synergistically drive the competition and evolution of aquatic microbial communities, and their resistance and resilience, of which experimental evidences remain scarce. In this study, laboratory sediment-water column experiments were employed to mimic the organic carbon-driven water blackening and odorization process in urban rivers and to elucidate impacts of DOC on the microbial ecology stability. Results showed that low DOC (25-75 mg/L TOC) and high DOC (100-150 mg/L TOC) changed the aquatic microbial community assemblies in different patterns: (1) the low DOC enriched K-selection microorganisms (e.g., bacteria and predators) with low biomass and low resilience, as well as high resistance to perturbations in changing microbial community assemblies; (2) the high DOC was associated with r-selection microorganisms with high biomass and improved resilience, together with low resistance detrimental to microbial ecology stability. Overall, this study provided new insights into impacts of DOC on aquatic microbial ecology stability, which may guide sustainable urban river management.

scholarly journals Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

2018 ◽  
Author(s):  
Maozhen Han ◽  
Melissa Dsouza ◽  
Chunyu Zhou ◽  
Hongjun Li ◽  
Junqian Zhang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Agricultural Pollution ◽  
Agricultural Activities ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Honghu Lake

AbstractBackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

scholarly journals Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

2021 ◽  
Vol 12 ◽  
Author(s):  
Lauren M. Lui ◽  
Erica L.-W. Majumder ◽  
Heidi J. Smith ◽  
Hans K. Carlson ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Data Types ◽  
Modeling Framework ◽  
Rapid Acquisition ◽  
Mechanistic Understanding ◽  
And Function

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

scholarly journals METABOLIC: High-throughput Profiling of Microbial Genomes for Functional Traits, Biogeochemistry, and Community-scale Metabolic Networks

2020 ◽  
Author(s):  
Zhichao Zhou ◽  
Patricia Q Tran ◽  
Adam M Breister ◽  
Yang Liu ◽  
Kristopher Kieft ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Single Cell ◽  
Metabolic Networks ◽  
Biogeochemical Cycling ◽  
Microbial Interactions ◽  
Microbial Genomes ◽  
Biogeochemical Models ◽  
Genome Scale

Abstract Background: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent, however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and contributions to biogeochemical cycling. Results: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, identification of metabolism markers, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the community, potential microbial metabolic handoffs and metabolite exchange, and calculation of microbial community contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or from single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, and community-scale metabolic networks using a newly defined metric ‘MN-score’ (metabolic network score). METABOLIC takes ~3 hours with 40 CPU threads to process ~100 genomes and metagenomic reads within which the most compute-demanding part of hmmsearch takes ~45 mins, while it takes ~5 hours to complete hmmsearch for ~3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.Conclusion: METABOLIC enables consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available at https://github.com/AnantharamanLab/METABOLIC under GPLv3.

scholarly journals Evaluation of DESS as a storage medium for microbial community analysis

2018 ◽  
Author(s):  
Kevin M Lee ◽  
Madison Adams ◽  
Jonathan L Klassen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Microbial Community Structure ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ant Colonies ◽  
And Storage ◽  
Phosphate Buffered Saline

Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test the ability of these preservatives to maintain the structure of fungus garden microbial communities. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.

scholarly journals TROPHIC AND NUTRIENT DYNAMIC ASPECT OF AQUATIC MICROBIAL ECOLOGY

1970 ◽  
Vol 17 ◽  
pp. 9-16
Author(s):  
Tek Bahadur Gurung ◽  
Jotaro Urabe
Keyword(s):  
Organic Carbon ◽  
Microbial Ecology ◽  
Trophic Level ◽  
Aquatic Ecosystem ◽  
Nutrient Dynamics ◽  
Heterotrophic Bacteria ◽  
Limiting Factor ◽  
Aquatic Microbial Ecology ◽  
Nutrient Dynamic

This paper gives a chronological review on our understanding in the role of heterotrophic bacteria in trophic and nutrient dynamic aspects of aquatic microbial ecology. Traditionally, the role of  heterotrophic bacteria was known as decomposer only. Later studies revealed that bacteria could be the food for several grazers especially, nano-, micro-  and mesozooplankton. Now, it is clear that heterotrophic bacteria channel the energy and matter to higher trophic level via microbial and metazoan food chains. Previously it was argued that dissolved organic carbon (DOC) is the prime limiting factor for fueling the energy and nutrient in aquatic ecosystem. However, emerging experimental evidences suggest that enrichment of plant nutrients such as phosphorus (P) stimulates bacterial growth. These suggest accumulation or organic carbon and other important nutrients in aquatic ecosystem, which are funneled in presence of limiting nutrients phosphorus. Moreover, recent studies showed that material transfer efficiency from bacteria to higher trophic level may depend on species composition of mesozooplankton. These discoveries established that bacterial primary production contributes substantially in secondary production, implying that contrasting to their tiny form bacteria play much important role in trophic and nutrient dynamics aspects of aquatic ecology. Key words:  Heterotrophic bacteria; Trophic dynamics; Nutrients; Mesozooplankton DOI: 10.3126/eco.v17i0.4097Ecoprint An International Journal of Ecology Vol. 17, 2010 Page: 9-16 Uploaded date: 28 December, 2010  

scholarly journals Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

2017 ◽  
Vol 83 (16) ◽  
Author(s):  
Noah Stern ◽  
Matthew Ginder-Vogel ◽  
James C. Stegen ◽  
Evan Arntzen ◽  
David W. Kennedy ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Water ◽  
Hyporheic Zone ◽  
Columbia River ◽  
Fluid Source ◽  
Hydrologic Exchange

ABSTRACT Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situ colonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection during in situ colonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCE The influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.

scholarly journals Kinetics and identities of extracellular peptidases in subsurface sediments of the White Oak River Estuary, NC

2016 ◽  
Author(s):  
Andrew D. Steen ◽  
Richard T. Kevorkian ◽  
Jordan T. Bird ◽  
Nina Dombrowski ◽  
Brett J. Baker ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
River Estuary ◽  
Estuarine Sediments ◽  
White Oak ◽  
Organic Carbon Burial ◽  
Subsurface Sediments ◽  
Extracellular Peptidases

AbstractAnoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily slow rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per cell basis was approximately the same at all depths. Half-saturation constants (Km) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (D-phenylalanine and L-ornithine) increased relative to enzymes that act on L-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.ImportanceBurial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. Here we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.

scholarly journals Community coalescence: an eco-evolutionary perspective

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190252 ◽  
Author(s):  
Meaghan Castledine ◽  
Pawel Sierocinski ◽  
Daniel Padfield ◽  
Angus Buckling
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Evolutionary Dynamics ◽  
Species Interaction ◽  
Evolutionary Perspective ◽  
Theme Issue ◽  
Microbial Community Ecology ◽  
And Function ◽  
Crucial Characteristic

Community coalescence, the mixing of different communities, is widespread throughout microbial ecology. Coalescence can result in approximately equal contributions from the founding communities or dominance of one community over another. These different outcomes have ramifications for community structure and function in natural communities, and the use of microbial communities in biotechnology and medicine. However, we have little understanding of when a particular outcome might be expected. Here, we integrate existing theory and data to speculate on how a crucial characteristic of microbial communities—the type of species interaction that dominates the community—might affect the outcome of microbial community coalescence. Given the often comparable timescales of microbial ecology and microevolution, we explicitly consider ecological and evolutionary dynamics, and their interplay, in determining coalescence outcomes. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals Effects of Thinning on Microbial Community Structure in the Organic Horizon of Chinese Pine Plantations in Badaling, Beijing, China

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 828 ◽  
Author(s):  
Wang ◽  
Zhao ◽  
Sun ◽  
Yang ◽  
Zhou
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Pine Plantations ◽  
Pinus Tabulaeformis ◽  
Organic Horizon ◽  
Moderate Intensity ◽  
Chinese Pine

Research Highlights: Moderate thinning can effectively improve forestry production and change the microenvironment of understory vegetation. Background and Objectives: Microbial communities control the decomposition and transformation of forest organic matter; however, the influence of thinning on microbes in the organic horizon remains unclear. Materials and Methods: In this study, we subjected four plots of Chinese pine plantations in Badaling, Beijing to different thinning intensities, including no thinning (T0), low-intensity thinning (T10), medium-intensity thinning (T20), and high-intensity thinning (T50). The changes in chemical properties and microbial community compositions observed in the organic horizon, which comprised undecomposed litter (L layer) and half-decomposed litter (F layer), were analyzed after thinning. Microbial community compositions were evaluated using phospholipid fatty acid (PLFA) methods. Results: The results showed that the abundances of gram-negative bacteria (GN) and total bacteria (B) under the T10 thinning condition were the highest among the four thinning intensities, and the abundance of arbuscular mycorrhizal fungi (AMF) in T20 was higher than under other thinning intensities. The abundance of gram-positive bacteria (GP) and actinobacteria (ACT) in T10 was lower than in both T0 and T50. The abundance of total PLFAs and fungi (FU) was higher in the L layer, whereas the abundance of GP, GN, B, ACT, and AMF was higher in the F layer. Conclusions: Our results demonstrated that the L layer better reflects the influence of thinning on litter. Redundancy analysis (RDA) results indicated that the organic carbon (LOC) , dissolved organic carbon (DOC), and ammonium nitrogen (NH4+-N)contents of litter were primarily responsible for the observed changes in microbial community structure, with LOC alone explaining 62.6% of the total variance among the litter substrate factors selected. Overall, moderate-intensity thinning of Pinus tabulaeformis Carr. plantations created more favorable conditions for microbial communities in the organic horizon.

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