Taxonomic diversity and metabolic activity of microbial communities in rivers and estuarine waters of Southern Baikal in summer

2021 ◽  
Author(s):  
T.I. Zemskaya ◽  
S.V. Bukin ◽  
Y.S. Bukin ◽  
S.M. Chernitsina ◽  
T.V. Pogodaeva ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Activity ◽  
Taxonomic Diversity ◽  
Estuarine Waters

scholarly journals Functional metagenomic analysis of dust-associated microbiomes above the Red Sea

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nojood A. Aalismail ◽  
David K. Ngugi ◽  
Rubén Díaz-Rúa ◽  
Intikhab Alam ◽  
Michael Cusack ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Sequences ◽  
Biofilm Formation ◽  
Atmospheric Transport ◽  
Taxonomic Diversity ◽  
Functional Metagenomics ◽  
Genetic Traits ◽  
Gene Catalogue ◽  
Range Transport ◽  
Genes Encoding

Abstract Atmospheric transport is a major vector for the long-range transport of microbial communities, maintaining connectivity among them and delivering functionally important microbes, such as pathogens. Though the taxonomic diversity of aeolian microorganisms is well characterized, the genomic functional traits underpinning their survival during atmospheric transport are poorly characterized. Here we use functional metagenomics of dust samples collected on the Global Dust Belt to initiate a Gene Catalogue of Aeolian Microbiome (GCAM) and explore microbial genetic traits enabling a successful aeolian lifestyle in Aeolian microbial communities. The GCAM reported here, derived from ten aeolian microbial metagenomes, includes a total of 2,370,956 non-redundant coding DNA sequences, corresponding to a yield of ~31 × 106 predicted genes per Tera base-pair of DNA sequenced for the aeolian samples sequenced. Two-thirds of the cataloged genes were assigned to bacteria, followed by eukaryotes (5.4%), archaea (1.1%), and viruses (0.69%). Genes encoding proteins involved in repairing UV-induced DNA damage and aerosolization of cells were ubiquitous across samples, and appear as fundamental requirements for the aeolian lifestyle, while genes coding for other important functions supporting the aeolian lifestyle (chemotaxis, aerotaxis, germination, thermal resistance, sporulation, and biofilm formation) varied among the communities sampled.

scholarly journals Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Jeffrey J Marlow ◽  
Isabella Colocci ◽  
Sean P Jungbluth ◽  
Nils Moritz Weber ◽  
Amy Gartman ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Metabolic Activity ◽  
Point Sources ◽  
Emergent Properties ◽  
Spatial Relationships ◽  
Environmental Regime ◽  
Novel Approach ◽  
Stable Conditions ◽  
Metabolite Exchange

ABSTRACT Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities ‘as they really are’ and explore determinants of metabolic activity across a range of microbiomes.

Environmental microbiology: biodegradation

1982 ◽  
Vol 297 (1088) ◽  
pp. 575-597 ◽  
Keyword(s):  
Microbial Communities ◽  
Metabolic Activity ◽  
Metabolic Pathways ◽  
Environmental Microbiology ◽  
Single Species ◽  
Natural Compounds ◽  
Synthetic Compounds ◽  
Metabolic Versatility ◽  
Xenobiotic Compounds

A genuinely new dimension to microbiology concerns the fate of synthetic compounds dispersed throughout the biosphere, with xenobiotic compounds representing a major challenge to the metabolic versatility of microorganisms. While microbial bio-degradation of many of these compounds proceeds by the activity of single species of microorganisms, this paper develops the argument that microbial communities function by synergistic mechanisms to effect the breakdown of many of these compounds. The degradation of some compounds, especially xenobiotic compounds, depends on the use of gratuitous metabolic pathways evolved for natural compounds, which in many instances may be evolved through the combined metabolic activity of two or more microorganisms. The role of plasmid coded pathways is also considered in the context of the evolution of novel pathways.

scholarly journals Metabolic dominance of bivalves predates brachiopod diversity decline by more than 150 million years

2014 ◽  
Vol 281 (1783) ◽  
pp. 20133122 ◽  
Author(s):  
Jonathan L. Payne ◽  
Noel A. Heim ◽  
Matthew L. Knope ◽  
Craig R. McClain
Keyword(s):  
Body Size ◽  
Metabolic Activity ◽  
Energy Use ◽  
Taxonomic Diversity ◽  
Metabolic Rates ◽  
Geological Time ◽  
Numerical Abundance ◽  
Ecological Importance ◽  
Ecological Dominance ◽  
Size Data

Brachiopods and bivalves feed in similar ways and have occupied the same environments through geological time, but brachiopods were far more diverse and abundant in the Palaeozoic whereas bivalves dominate the post-Palaeozoic, suggesting a transition in ecological dominance 250 Ma. However, diversity and abundance data alone may not adequately describe key changes in ecosystem function, such as metabolic activity. Here, we use newly compiled body size data for 6066 genera of bivalves and brachiopods to calculate metabolic rates and revisit this question from the perspective of energy use, finding that bivalves already accounted for a larger share of metabolic activity in Palaeozoic oceans. We also find that the metabolic activity of bivalves has increased by more than two orders of magnitude over this interval, whereas brachiopod metabolic activity has declined by more than 50%. Consequently, the increase in bivalve energy metabolism must have occurred via the acquisition of new food resources rather than through the displacement of brachiopods. The canonical view of a mid-Phanerozoic transition from brachiopod to bivalve dominance results from a focus on taxonomic diversity and numerical abundance as measures of ecological importance. From a metabolic perspective, the oceans have always belonged to the clams.

scholarly journals Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Benjamin E. Wolfe
Keyword(s):  
Microbial Communities ◽  
Taxonomic Diversity ◽  
Fermented Food ◽  
Trophic Levels ◽  
Intraspecific Diversity ◽  
Sequencing Data ◽  
Molecular Approaches ◽  
Model Community ◽  
Microbiome Assembly

ABSTRACTAs troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimicin vitrocommunities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.

scholarly journals Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia)

Water ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 1899
Author(s):  
Mattia Saccò ◽  
Nicole E. White ◽  
Matthew Campbell ◽  
Sebastian Allard ◽  
William F. Humphreys ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Taxonomic Diversity ◽  
Aquatic Environments ◽  
Community Patterns ◽  
Hypersaline Lakes ◽  
Hypersaline Ecosystems ◽  
Water Columns ◽  
Dna Metabarcoding ◽  
Influential Parameters

Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.

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