scholarly journals An ensemble approach to the structure-function problem in microbial communities

iScience ◽  
2022 ◽  
pp. 103761
Author(s):  
Chandana Gopalakrishnappa ◽  
Karna Gowda ◽  
Kaumudi Prabhakara ◽  
Seppe Kuehn
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Ensemble Approach

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.

scholarly journals Functional Redundancy in Local Spatial Scale Microbial Communities Suggest Stochastic Processes at an Urban Wilderness Preserve in Austin, TX, USA

2020 ◽  
Author(s):  
Justin Stewart ◽  
Amy Ontai ◽  
Kizil Yusoof ◽  
Teresa Bilinski
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Structure Function ◽  
Microbial Communities ◽  
Spatial Scale ◽  
Spatial Scales ◽  
Substrate Utilization ◽  
Carbon Substrate ◽  
Utilization Patterns ◽  
Edaphic Properties

AbstractEmpirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales, however; less is known as smaller spatial scales (e.g 10s-100s of meters). The goal of this research was to evaluate the relationship between ecosystem characteristics and bacterial community structure/function in soils across small spatial scales in an urban preserve. We employed 16s rRNA gene sequencing, community level physiological profiling (CLPP), and soil chemical analysis to address this goal. We found no significant relationship between gradients in soil characteristics and community structure/function. In contrast, Acidobacteria, Bacteroidetes, and Nitrospirae responded to variation in edaphic properties. Taxa exhibited a wide range in dispersal, supporting our finding of community wide differences in taxonomy. Furthermore, there was high metabolic diversity within the bacterial communities despite preferential metabolism of water-soluble polymers (Tween 40/80). Carbon substrate utilization patterns also suggest dominance of functional generalists. Pairwise comparison of carbon substrate utilization patterns indicates that there are high levels of microbial functional redundancy within soils across the sampling area. Lastly, we found that edaphic properties did not shape the overall community structure and/or function, and our analyses suggest that stochasticity may play a role in bacterial community assembly in soils with the local spatial scale of this research study.Graphical AbstractOne Sentence Summary: Microorganisms at small spatial scales were functionally similar despite subtle differences in community composition.

scholarly journals Directed evolution of microbial communities

2020 ◽  
Author(s):  
Alvaro Sanchez ◽  
Jean C. C. Vila ◽  
Chang-Yu Chang ◽  
Juan Diaz-Colunga ◽  
Sylvie Estrela ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Directed Evolution ◽  
Functional Traits ◽  
Artificial Selection ◽  
Genetic Variants ◽  
Top Down ◽  
Guided Exploration ◽  
Practical Guidelines ◽  
Genotype Space

Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. Here, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes, and discuss how the tools of directed evolution may be deployed to engineer communities from the top-down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape, and propose practical guidelines for navigating these ecological landscapes.

scholarly journals Functional redundancy in local spatial scale microbial communities suggests stochastic processes at an urban wilderness preserve in Austin, TX, USA

2021 ◽  
Vol 368 (3) ◽  
Author(s):  
Justin D. Stewart ◽  
Amy Ontai ◽  
Kizil Yusoof ◽  
Kelly S. Ramirez ◽  
Teresa Bilinski
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Structure Function ◽  
Microbial Communities ◽  
Carbon Metabolism ◽  
Spatial Scales ◽  
Soil Microbial Communities ◽  
Functional Redundancy ◽  
Rrna Gene ◽  
Edaphic Properties

ABSTRACT Empirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales; however, less is known at smaller spatial scales. The goal of this research was to evaluate relationships between ecosystem characteristics and bacterial community structure/function at broad taxonomic resolutions in soils across small spatial scales. We employed 16S rRNA gene sequencing, community-level physiological profiling and soil chemical analysis to address this goal. We found weak relationships between gradients in soil characteristics and community structure/function. Specific operational taxonomic units did not respond to edaphic variation, but Acidobacteria, Bacteroidetes and Nitrospirae shifted their relative abundances. High metabolic diversity within the bacterial communities was observed despite general preference of Tween 40/80. Carbon metabolism patterns suggest dominance of functional specialists at our times of measurement. Pairwise comparison of carbon metabolism patterns indicates high levels of functional redundancy. Lastly, at broad taxonomic scales, community structure and function weakly covary with edaphic properties. This evidence suggests that stochasticity or unmeasured environmental gradients may be influential in bacterial community assembly in soils at small spatial scales.

scholarly journals Structure, function and resilience to desiccation of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve, Rondonia)

2019 ◽  
Vol 21 (5) ◽  
pp. 1702-1717 ◽  
Author(s):  
Marcela Hernández ◽  
Melanie Klose ◽  
Peter Claus ◽  
David Bastviken ◽  
Humberto Marotta ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Amazon Rainforest

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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