scholarly journals The microbial exometabolome: ecological resource and architect of microbial communities

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190250 ◽  
Author(s):  
Angela E. Douglas
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Priority Effects ◽  
Future Research ◽  
Metabolic Efficiency ◽  
Total Biomass ◽  
Ecological Processes ◽  
Evolutionary Diversification ◽  
Metabolite Exchange ◽  
Starting Conditions

All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals Regular Biochar and Bacteria-Inoculated Biochar Alter the Composition of the Microbial Community in the Soil of a Chinese Fir Plantation

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 951
Author(s):  
Liguo Song ◽  
Lingyu Hou ◽  
Yongqiang Zhang ◽  
Zhichao Li ◽  
Wenzheng Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Principal Component ◽  
Nutrient Content ◽  
Chinese Fir ◽  
Bulk Soil ◽  
Ecological Processes ◽  
Chinese Fir Plantation

Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.

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.

scholarly journals Reconciling Ecological and Engineering Design Principles for Building Microbiomes

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Hans C. Bernstein
Keyword(s):  
Microbial Communities ◽  
Engineering Design ◽  
Environmental Sustainability ◽  
Environmental Filtering ◽  
Design Principles ◽  
Priority Effects ◽  
Interspecies Interactions ◽  
Ecological Processes ◽  
Natural Processes ◽  
And Control

ABSTRACT Simplified microbial communities, or “benchtop microbiomes,” enable us to manage the profound complexity of microbial ecosystems. Widespread activities aiming to design and control communities result in novel resources for testing ecological theories and also for realizing new biotechnologies. There is much to be gained by reconciling engineering design principles with ecological processes that shape microbiomes in nature. In this short Perspective, I will address how natural processes such as environmental filtering, the establishment of priority effects, and community “blending” (coalescence) can be harnessed for engineering microbiomes from complex starting materials. I will also discuss how future microbiome architects may draw inspiration from modern practices in synthetic biology. This topic is based on an important overarching research goal, which is to understand how natural forces shape microbial communities and interspecies interactions such that new engineering design principles can be extracted to promote human health or energy and environmental sustainability.

scholarly journals Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers

mSystems ◽  
2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Robert E. Danczak ◽  
Michael D. Johnston ◽  
Chris Kenah ◽  
Michael Slattery ◽  
Michael J. Wilkins
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Null Model ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Internal Dynamics ◽  
Ecological Processes ◽  
Stable Conditions ◽  
Community Complexity

ABSTRACT Microbial ecological processes are frequently studied in the presence of perturbations rather than in undisturbed environments, despite the relatively stable conditions dominating many microbial habitats. To examine processes influencing microbial community structuring in the absence of strong external perturbations, three unperturbed aquifers in Ohio (Greene, Licking, and Athens) were sampled over 2 years and analyzed using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Redox conditions ranging from highly reducing to more oxidizing distinguished aquifer geochemistry across the three locations. Distinct microbial communities were present in each aquifer, and overall community structure was related to geochemistry, although community composition was more similar between the Athens and Licking locations. The ecological processes acting upon microbial assemblages within aquifers were varied; geochemical changes affected the Athens location, while time or some unknown factor affected Greene County. Stochastic processes, however, dominated the Licking aquifer, suggesting a decoupling between environmental fluctuations and community development. Although physicochemical differences might be expected to drive variable selection, dispersal limitation (inability to mix) explained differences between Athens and Licking. Finally, community complexity as measured by “cohesion” indicated that less-interconnected communities experienced higher turnover and were more likely to be affected by stochastic processes. Conversely, more-interconnected communities experienced lower turnover and susceptibility to homogenizing selection. Based upon these data, we support the hypothesis that unperturbed environments house dynamic microbial communities due to external and internal forces. IMPORTANCE Many microbial ecology studies have examined community structuring processes in dynamic or perturbed situations, while stable environments have been investigated to a lesser extent. Researchers have predicted that environmental communities never truly reach a steady state but rather exist in states of constant flux due to internal, rather than external, dynamics. The research presented here utilized a combined null model approach to examine the deterministic and stochastic processes responsible for observed community differences in unperturbed, groundwater ecosystems. Additionally, internal dynamics were investigated by relating a recently published measure of community complexity (cohesion) to ecological structuring processes. The data presented here suggest that communities that are more cohesive, and therefore more complex, are more likely affected by homogenizing selection, while less-complex communities are more susceptible to dispersal. By understanding the relationship between internal dynamics and community structuring processes, insight about microbial population development in natural systems can be obtained.

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.

scholarly journals Loss of a Single Plant Functional Group in Litter Had Marginal Impacts on Microbial Community Diversity and Composition in a Tibet Fir Forest

2021 ◽  
Author(s):  
Qianwei Li ◽  
Lifeng Wang ◽  
Yamei Chen ◽  
Li Guo ◽  
Chengming You ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Driving Forces ◽  
Community Diversity ◽  
Plant Functional Groups ◽  
Plant Residues ◽  
Microbial Composition ◽  
Ecological Processes ◽  
And Function

Abstract Aim The decomposition of plant residues is a fundamental process of soil organic matter accumulation. The loss of plant functional groups (PFGs) could affect this process by producing litter of different qualities in the soil. Microorganisms are one of the indispensable driving forces of ecological processes, but the mechanisms by microbial communities respond to aboveground PFG changes are still unclear, which limits our understanding of biogeochemical cycle changes under PFG loss.Methods We assessed the microbial taxonomic and functional composition of six typical single PFGs (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern), random loss of a single PFG (SPFG) from litter mixtures and total mixture of six PFGs in a Tibetan fir forest by a high-throughput sequencing method.Results The microbial composition and function did not change with loss of a SPFG in litter, and microbial communities were mainly determined by the carbon and nitrogen ratio (C:N), carbon and phosphorus ratio (C:P), N and lignin, and bacterial functional pathways and fungal functional guilds were both determined by N, C:N and C:P ratios. Bacterial diversity was positively related while fungal diversity was negatively related to N and cellulose concentrations.Conclusion We speculated that the difference in initial litter qualities (especially C:N) between different PFGs, rather than a decreased number of PFGs, is a determinant of microbial composition and function. As the loss of PFG does not change litter quality, the microbial community can resist the loss of PFG, which maintains alpine ecosystem carbon and nutrient cycling stability.

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 Collective efficacy and disorder through the eyes of neighbourhood inhabitants and key informants

2021 ◽  
pp. 147737082110006
Author(s):  
Wim Hardyns ◽  
Thom Snaphaan ◽  
Sara Willems ◽  
Lieven J. R. Pauwels
Keyword(s):  
Convergent Validity ◽  
Social Trust ◽  
Survey Method ◽  
Future Research ◽  
Ecological Stability ◽  
Organizational Processes ◽  
Ecological Processes ◽  
Key Informants ◽  
Analysis Technique ◽  
Key Informant

This study examines the ecological reliability, convergent validity and ecological stability of neighbourhood (dis)organizational processes measured by means of two methods: inhabitant surveys and the so-called key informant analysis technique. Considering that ecological processes play a major role in many contemporary criminological theories and research, it is vital to take into account methodological challenges and to question the reliability, validity and stability of the measures reflecting these underlying processes. (Dis)organizational processes are predominantly measured by means of questionnaires surveying neighbourhood inhabitants. To yield ecologically reliable and valid measures this approach requires large numbers of respondents. In this study we analyse the relationships between ecological measures of neighbourhood processes based on surveys of inhabitants versus key informants. The findings suggest that key informants can provide reliable, valid and stable measures of (dis)organizational neighbourhood processes. Therefore, the key informant analysis technique is an essential complementary, or even substitutive, method in the measurement of neighbourhood processes; shared survey-method variance is eliminated and it is possible to survey fewer key informants than inhabitants to obtain reliable and valid information on social trust and disorder. Nevertheless, this method is not suitable for measuring all neighbourhood processes, such as informal social control. Therefore, outstanding challenges and avenues for future research are discussed as well.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

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