scholarly journals Auxotrophic interactions: a stabilizing attribute of aquatic microbial communities?

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Winifred M Johnson ◽  
Harriet Alexander ◽  
Raven L Bier ◽  
Dan R Miller ◽  
Mario E Muscarella ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Theoretical Work ◽  
Microbial Interactions ◽  
Ecosystem Structure ◽  
Community Members ◽  
Aquatic Microorganisms ◽  
The Stability

ABSTRACT Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.

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.

scholarly journals Agricultural Conservation Practices and Aquatic Ecological Responses

Water ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 1687
Author(s):  
Richard E. Lizotte ◽  
Peter C. Smiley ◽  
Robert B. Gillespie ◽  
Scott S. Knight
Keyword(s):  
Aquatic Ecosystems ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Soil Health ◽  
Conservation Agriculture ◽  
Agricultural Runoff ◽  
The United States ◽  
Ecosystem Structure ◽  
Ecological Responses ◽  
And Function

Conservation agriculture practices (CAs) have been internationally promoted and used for decades to enhance soil health and mitigate soil loss. An additional benefit of CAs has been mitigation of agricultural runoff impacts on aquatic ecosystems. Countries across the globe have agricultural agencies that provide programs for farmers to implement a variety of CAs. Increasingly there is a need to demonstrate that CAs can provide ecological improvements in aquatic ecosystems. Growing global concerns of lost habitat, biodiversity, and ecosystem services, increased eutrophication and associated harmful algal blooms are expected to intensify with increasing global populations and changing climate. We conducted a literature review identifying 88 studies linking CAs to aquatic ecological responses since 2000. Most studies were conducted in North America (78%), primarily the United States (73%), within the framework of the USDA Conservation Effects Assessment Project. Identified studies most frequently documented macroinvertebrate (31%), fish (28%), and algal (20%) responses to riparian (29%), wetland (18%), or combinations (32%) of CAs and/or responses to eutrophication (27%) and pesticide contamination (23%). Notable research gaps include better understanding of biogeochemistry with CAs, quantitative links between varying CAs and ecological responses, and linkages of CAs with aquatic ecosystem structure and function.

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew A Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Fecal Samples ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

scholarly journals Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vanessa L. Brisson ◽  
Jennifer E. Schmidt ◽  
Trent R. Northen ◽  
John P. Vogel ◽  
Amélie C. M. Gaudin
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Agricultural System ◽  
Community Members ◽  
Genetic Groups ◽  
Maize Domestication ◽  
Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

scholarly journals Metatranscriptomic Evidence for Co-Occurring Top-Down and Bottom-Up Controls on Toxic Cyanobacterial Communities

2015 ◽  
Vol 81 (9) ◽  
pp. 3268-3276 ◽  
Author(s):  
Morgan M. Steffen ◽  
B. Shafer Belisle ◽  
Sue B. Watson ◽  
Gregory L. Boyer ◽  
Richard A. Bourbonniere ◽  
...  
Keyword(s):  
Microbial Community ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Lake Erie ◽  
Sequence Data ◽  
Top Down ◽  
Western Basin ◽  
Bottom Up ◽  
Content Type ◽  
Cyanobacterial Harmful Algal Blooms

ABSTRACTLittle is known about the molecular and physiological function of co-occurring microbes within freshwater cyanobacterial harmful algal blooms (cHABs). To address this, community metatranscriptomes collected from the western basin of Lake Erie during August 2012 were examined. Using sequence data, we tested the hypothesis that the activity of the microbial community members is independent of community structure. Predicted metabolic and physiological functional profiles from spatially distinct metatranscriptomes were determined to be ≥90% similar between sites. Targeted analysis ofMicrocystis aeruginosa, the historical causative agent of cyanobacterial harmful algal blooms over the past ∼20 years, as well as analysis ofPlanktothrix agardhiiandAnabaena cylindrica, revealed ongoing transcription of genes involved in microcystin toxin synthesis as well as the acquisition of both nitrogen and phosphorus, nutrients often implicated as independent bottom-up drivers of eutrophication in aquatic systems. Transcription of genes involved in carbon dioxide (CO2) concentration and metabolism also provided support for the alternate hypothesis that high-pH conditions and dense algal biomass result in CO2-limiting conditions that further favor cyanobacterial dominance. Additionally, the presence ofMicrocystis-specific cyanophage sequences provided preliminary evidence of possible top-down virus-mediated control of cHAB populations. Overall, these data provide insight into the complex series of constraints associated withMicrocystisblooms that dominate the western basin of Lake Erie during summer months, demonstrating that multiple environmental factors work to shape the microbial community.

scholarly journals Microbial and chemical dynamics of a toxic dinoflagellate bloom

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9493
Author(s):  
Nastassia V. Patin ◽  
Emily Brown ◽  
Gabriella Chebli ◽  
Claire Garfield ◽  
Julia Kubanek ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Economic Damage ◽  
Sequence Variant ◽  
Toxic Dinoflagellate ◽  
Bloom Formation ◽  
Intracellular Metabolite Pools ◽  
Domain Level ◽  
Dinoflagellate Bloom

Harmful Algal Blooms (HABs) exert considerable ecological and economic damage and are becoming increasingly frequent worldwide. However, the biological factors underlying HABs remain uncertain. Relationships between algae and bacteria may contribute to bloom formation, strength, and duration. We investigated the microbial communities and metabolomes associated with a HAB of the toxic dinoflagellate Karenia brevis off the west coast of Florida in June 2018. Microbial communities and intracellular metabolite pools differed based on both bacterial lifestyle and bloom level, suggesting a complex role for blooms in reshaping microbial processes. Network analysis identified K. brevis as an ecological hub in the planktonic ecosystem, with significant connections to diverse microbial taxa. These included four flavobacteria and one sequence variant unidentified past the domain level, suggesting uncharacterized diversity in phytoplankton-associated microbial communities. Additionally, intracellular metabolomic analyses associated high K. brevis levels with higher levels of aromatic compounds and lipids. These findings reveal water column microbial and chemical characteristics with potentially important implications for understanding HAB onset and duration.

scholarly journals Cohesiveness in microbial community coalescence

2018 ◽  
Author(s):  
Nanxi Lu ◽  
Alicia Sanchez-Gorostiaga ◽  
Mikhail Tikhonov ◽  
Alvaro Sanchez
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Empirical Work ◽  
Invasion Success ◽  
Community Members ◽  
Interacting Species ◽  
Resource Interactions ◽  
Different Origins ◽  
Microbial Community Assembly ◽  
Selection Of

AbstractMicrobial invasions exhibit many unique properties; notably, entire microbial communities often invade one another, a phenomenon known as community coalescence. In spite of the potential importance of this process for the dynamics and stability of microbiome assembly, our understanding of it is still very limited. Recent theoretical and empirical work has proposed that large microbial communities may exhibit an emergent cohesiveness, as a result of collective consumer-resource interactions and metabolic feedbacks between microbial growth and the environment. A fundamental prediction of this proposal is the presence of ecological co-selection during community coalescence, where the invasion success of a given taxon is determined by its community members. To establish the generality of this prediction in experimental microbiomes, we have performed over one hundred invasion and coalescence experiments with environmental communities of different origins that had spontaneously and stably assembled in two different synthetic aerobic environments. We show that the dominant species of the coalesced communities can both recruit their community members (top-down co-selection) and be recruited by them (bottom-up co-selection) into the coalesced communities. Our results provide direct evidence that collective invasions generically produce ecological co-selection of interacting species, emphasizing the importance of community-level interactions during microbial community assembly.

scholarly journals How sample heterogeneity can obscure the signal of microbial interactions

2019 ◽  
Author(s):  
David W. Armitage ◽  
Stuart E. Jones
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Species Interactions ◽  
Dynamic Models ◽  
Spatial Scales ◽  
Microbial Interactions ◽  
Vital Rates ◽  
Ecological Processes ◽  
Correlation Networks ◽  
Community Data

ABSTRACTMicrobial community data are commonly subjected to computational tools such as correlation networks, null models, and dynamic models, with the goal of identifying the ecological processes structuring microbial communities. Researchers applying these methods assume that the signs and magnitudes of species interactions and vital rates can be reliably parsed from observational data on species’ (relative) abundances. However, we contend that this assumption is violated when sample units contain any underlying spatial structure. Here, we show how three phenomena — Simpson’s paradox, context-dependence, and nonlinear averaging — can lead to erroneous conclusions about population parameters and species interactions when samples contain heterogeneous mixtures of populations or communities. At the root of this issue is the fundamental mismatch between the spatial scales of species interactions (micrometres) and those of typical microbial community samples (millimetres to centimetres). These issues can be overcome by measuring and accounting for spatial heterogeneity at very small scales, which will lead to more reliable inference of the ecological mechanisms structuring natural microbial communities.

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