scholarly journals Microbial Function and Hydrochemistry within a Stratified Anchialine Sinkhole: A Window into Coastal Aquifer Interactions

Water ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 972 ◽  
Author(s):  
Madison Davis ◽  
James Garey
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Coastal Aquifer ◽  
Sulfide Oxidation ◽  
Mixing Zone ◽  
Mixing Processes ◽  
Community Function ◽  
Bioinformatic Tools ◽  
Floridan Aquifer ◽  
Aquifer Systems

Anchialine sinkholes provide insight into coastal aquifer systems and coastal mixing processes. Aquifer microbial community function is usually inferred from hydrochemical information, but there are few direct studies of microbial communities in the Floridan Aquifer. Hospital Hole is a 43 m-deep stratified sinkhole under the Weeki Wachee River, FL, with three distinct brackish layers: a hypoxic layer, a chemocline and a sulfidic anoxic layer. Illumina sequencing and bioinformatic tools were used to reconstruct metabolic functions and interactions of microbial communities in each layer. Each layer appears to originate from different parts of the coastal mixing zone and has a distinct microbial community with unique functions, which are influenced by the respective hydrochemistry. Sulfide oxidation and nitrate reduction are the most abundant functions. Syntrophy between methane oxidizers, methanogens and sulfate reducers is present. Similarities between the hydrochemistry and potential connectivity of Hospital Hole and the Floridan Aquifer coastal mixing zone suggest that microbial communities of Hospital Hole could be a surrogate for the coastal mixing zone of the aquifer in the absence of direct studies. Understanding how groundwater microbial communities react to saltwater intrusion and nutrient flux will be useful in predicting how coastal aquifer regions might react to anthropogenic change.

scholarly journals Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

2017 ◽  
Vol 14 (23) ◽  
pp. 5403-5424 ◽  
Author(s):  
Minsu Kim ◽  
Dani Or
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Mechanistic Model ◽  
Soil Surface ◽  
Hydration Status ◽  
Carbon And Nitrogen ◽  
Community Function ◽  
Diurnal Cycles ◽  
Biogeochemical Fluxes ◽  
Biogeochemical Hotspots

Abstract. Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

scholarly journals Temporal and spatial mediated changes in subsurface microbial community assemblages and functions

2020 ◽  
Author(s):  
Madison C. Davis
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Change ◽  
Central Florida ◽  
Bioinformatic Tools ◽  
Metabolic Functions ◽  
Large Perturbation ◽  
Groundwater Ecosystems ◽  
Community Assemblages ◽  
Temporal And Spatial

Abstract. Groundwater ecosystems can host different habitats with unique microbial assemblages and functions. Although groundwater microbes are important to subsurface processes, little is known about the drivers of change in these communities. Illumina sequencing and bioinformatic tools were used to examine whether different groundwater zones could have the same patterns of microbial community change over a two-year period. Five different groundwater zones from Hospital Hole, a stratified sinkhole in west-central Florida, were used in this study since they have been previously shown to host distinct microbial communities. Seasonal patterns of microbial community assemblages and potential metabolic functions were not identified in the sinkhole communities. Different physicochemical parameters correlated to microbial community change within each zone. Local hydrogeology appears to play an important role in subsurface microbial community change since Hurricane Irma and seasonal turnover events did not appear to cause a large perturbation in the microbial communities. Nutrient availability and local hydrogeochemistry appear to be important drivers of microbial community change in the subsurface.

scholarly journals Predicting the structure and function of coalesced microbial communities

2017 ◽  
Author(s):  
Pawel Sierocinski ◽  
Kim Milferstedt ◽  
Florian Bayer ◽  
Tobias Großkopf ◽  
Mark Alston ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Methane Production ◽  
Structure And Function ◽  
Recent Theory ◽  
Simple Method ◽  
Average Performance ◽  
Community Function ◽  
And Function

ABSTRACTMicrobial communities commonly coalesce in nature, but the consequences for resultant community structure and function is unclear. Consistent with recent theory, we demonstrate using methanogenic communities that the most productive communities in isolation dominated when communities were mixed. As a corollary of this dynamic, total methane production increased with the number of inoculated communities. The cohesion and dominance of single communities was explained by more “niche-packed” communities being both more efficient at exploiting resources and resistant to invasion, rather than a function of the average performance of component species. These results are likely to be relevant to the ecological dynamics of natural microbial communities, as well as demonstrating a simple method to predictably enhance microbial community function in biotechnology, health and agriculture.

scholarly journals Anaerobic Decomposition of Switchgrass by Tropical Soil-Derived Feedstock-Adapted Consortia

mBio ◽  
2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Kristen M. DeAngelis ◽  
Julian L. Fortney ◽  
Sharon Borglin ◽  
Whendee L. Silver ◽  
Blake A. Simmons ◽  
...  
Keyword(s):  
Microbial Community ◽  
Tropical Forest ◽  
Microbial Communities ◽  
Forest Soils ◽  
Cloud Forest ◽  
Electron Acceptors ◽  
Biofuel Production ◽  
Microbial Consortia ◽  
Microbial Community Function ◽  
Community Function

ABSTRACTTropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of theFirmicutes,Bacteroidetes, andAlphaproteobacteriaas dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure.IMPORTANCEAfter multiple transfers, we established microbial consortia derived from two tropical forest soils with different native redox conditions. Communities derived from the rapidly fluctuating redox environment maintained a capacity to use added terminal electron acceptors (TEAs) after multiple transfers, though they were not present during the enrichment. Communities derived from lower-redox soils were not responsive to TEA addition but were much more efficient at switchgrass decomposition. Though the communities were different, diversity was not, and both were dominated by many of the same species of clostridia. This reflects the inadequacy of rRNA for determining the function of microbial communities, in this case the retained ability to utilize TEAs that were not part of the selective growth conditions. More importantly, this suggests that microbial community function is shaped by life history, where environmental factors produce heritable traits through natural selection over time, creating variation in the community, a phenomenon not well documented for microbes.

scholarly journals Reducing fluctuations in species composition facilitates artificial selection of microbial community function

2018 ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Community ◽  
Species Composition ◽  
Microbial Communities ◽  
Cell Sorting ◽  
Maturation Time ◽  
Experimental Procedure ◽  
Community Function ◽  
Stochastic Fluctuations ◽  
Total Product ◽  
Selection Of

AbstractMulti-species microbial communities often display functions - biochemical activities unattainable by member species alone, such as fighting pathogens. To improve community function, we can artificially select communities by growing “Newborn” communities over “maturation time” into “Adult” communities, and selecting highest-functioning Adults to “reproduce” by diluting each into multiple Newborns of the next cycle. Community selection has been attempted a few times on complex communities, often generating mixed results that are difficult to interpret. Here, we ask how costly community function may be improved via mutations and community selection. We simulate selection of two-species communities where Helpers digest Waste and generate Byproduct essential to Manufacturers; Manufacturers divert a fraction of their growth to make Product. Community function, the total Product in an “Adult”, is sub-optimal even when both species have been pre-optimized as monocultures. If we dilute an Adult into Newborns by pipetting (a common experimental procedure), stochastic fluctuations in Newborn composition prevents community function from improving. Reducing fluctuations via cell sorting allows selection to work. Our conclusions hold regardless of whether H and M are commensal or mutualistic, or variations in model assumptions.

scholarly journals Patterns of Microbially Driven Carbon Cycling in the Ocean: Links between Extracellular Enzymes and Microbial Communities

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Carol Arnosti
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Carbon Cycling ◽  
Large Scale ◽  
Extracellular Enzymes ◽  
Microbial Community Composition ◽  
Deep Ocean ◽  
Community Function ◽  
Enzymatic Function ◽  
Depth Gradients

Heterotrophic microbial communities play a central role in the marine carbon cycle. They are active in nearly all known environments, from the surface to the deep ocean, in the sediments, and from the equator to the Poles. In order to process complex organic matter, these communities produce extracellular enzymes of the correct structural specificity to hydrolyze substrates to sizes sufficiently small for uptake. Extracellular enzymatic hydrolysis thus initiates heterotrophic carbon cycling. Our knowledge of the enzymatic capabilities of microbial communities in the ocean is still underdeveloped. Recent studies, however, suggest that there may be large-scale patterns of enzymatic function in the ocean, patterns of community function that may be connected to emerging patterns of microbial community composition. Here I review some of these large-scale contrasts in microbial enzyme activities, between high-latitude and temperate surface ocean waters, contrasts between inshore and offshore waters, changes with depth gradients in the ocean, and contrasts between the water column and underlying sediments. These contrasting patterns are set in the context of recent studies of microbial communities and patterns of microbial biogeography. Focusing on microbial community function as well as composition and potential should yield clearer understanding of the factors driving carbon cycling in the ocean.

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 Investigating Groundwater Condition and Seawater Intrusion Status in Coastal Aquifer Systems of Eastern India

Water ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 1952
Author(s):  
Subrata Halder ◽  
Lingaraj Dhal ◽  
Madan K. Jha
Keyword(s):  
Groundwater Quality ◽  
Seawater Intrusion ◽  
Groundwater Level ◽  
Coastal Aquifer ◽  
Quality Data ◽  
Confined Aquifer ◽  
Groundwater Levels ◽  
Post Monsoon ◽  
Aquifer Systems ◽  
Sustainable Water Supply

Providing sustainable water supply for domestic needs and irrigated agriculture is one of the most significant challenges for the current century. This challenge is more daunting in coastal regions. Groundwater plays a pivotal role in addressing this challenge and hence, it is under growing stress in several parts of the world. To address this challenge, a proper understanding of groundwater characteristics in an area is essential. In this study, spatio-temporal analyses of pre-monsoon and post-monsoon groundwater-levels of two coastal aquifer systems (upper leaky confined and underlying confined) were carried out in Purba Medinipur District, West Bengal, India. Trend analysis of seasonal groundwater-levels of the two aquifers systems was also performed using Mann-Kendall test, Linear Regression test, and Innovative Trend test. Finally, the status of seawater intrusion in the two aquifers was evaluated using available groundwater-quality data of Chloride (Cl−) and Total Dissolve Solids (TDS). Considerable spatial and temporal variability was found in the seasonal groundwater-levels of the two aquifers. Further, decreasing trends were spotted in the pre-monsoon and post-monsoon groundwater-level time series of the leaky confined and confined aquifers, except pre-monsoon groundwater-levels in Contai-I and Deshpran blocks, and the post-monsoon groundwater-level in Ramnagar-I block for the leaky confined aquifer. The leaky confined aquifer in Contai-I, Contai-III, and Deshpran blocks and the confined aquifer in Nandigram-I and Nandigram-II blocks are vulnerable to seawater intrusion. There is an urgent need for the real-time monitoring of groundwater-levels and groundwater quality in both the aquifer systems, which can ensure efficient management of coastal groundwater reserves.

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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