Microbial community and bioelectrochemical activities in MFC for degrading phenol and producing electricity: Microbial consortia could make differences

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

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System Performance Corresponding to Bacterial Community Succession after a Disturbance in an Autotrophic Nitrogen Removal Bioreactor

mSystems ◽

10.1128/msystems.00398-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Hsiao-Pei Lu ◽

Yung-Hsien Shao ◽

Jer-Horng Wu ◽

Chih-hao Hsieh

Keyword(s):

Time Series ◽

Microbial Community ◽

System Performance ◽

Time Series Data ◽

Microbial Consortia ◽

Series Data ◽

Resolution Time ◽

Physicochemical Variables ◽

System Functioning ◽

Fine Resolution

ABSTRACT Performance of a bioreactor is affected by complex microbial consortia that regulate system functional processes. Studies so far, however, have mainly emphasized the selective pressures imposed by operational conditions (i.e., deterministic external physicochemical variables) on the microbial community as well as system performance, but have overlooked direct effects of the microbial community on system functioning. Here, using a bioreactor with ammonium as the sole substrate under controlled operational settings as a model system, we investigated succession of the bacterial community after a disturbance and its impact on nitrification and anammox (anaerobic ammonium oxidation) processes with fine-resolution time series data. System performance was quantified as the ratio of the fed ammonium converted to anammox-derived nitrogen gas (N2) versus nitrification-derived nitrate (npNO3−). After the disturbance, the N2/npNO3− ratio first decreased, then recovered, and finally stabilized until the end. Importantly, the dynamics of N2/npNO3− could not be fully explained by physicochemical variables of the system. In comparison, the proportion of variation that could be explained substantially increased (tripled) when the changes in bacterial composition were taken into account. Specifically, distinct bacterial taxa tended to dominate at different successional stages, and their relative abundances could explain up to 46% of the variation in nitrogen removal efficiency. These findings add baseline knowledge of microbial succession and emphasize the importance of monitoring the dynamics of microbial consortia for understanding the variability of system performance. IMPORTANCE Dynamics of microbial communities are believed to be associated with system functional processes in bioreactors. However, few studies have provided quantitative evidence. The difficulty of evaluating direct microbe-system relationships arises from the fact that system performance is affected by convolved effects of microbiota and bioreactor operational parameters (i.e., deterministic external physicochemical forcing). Here, using fine-resolution time series data (daily sampling for 2 months) under controlled operational settings, we performed an in-depth analysis of system performance as a function of the microbial community in the context of bioreactor physicochemical conditions. We obtained statistically evaluated results supporting the idea that monitoring microbial community dynamics could improve the ability to predict system functioning, beyond what could be explained by operational physicochemical variables. Moreover, our results suggested that considering the succession of multiple bacterial taxa would account for more system variation than focusing on any particular taxon, highlighting the need to integrate microbial community ecology for understanding system functioning.

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Ferrihydrite associated organic matter (OM) stimulates reduction by <i>Shewanella oneidensis</i> MR-1 and a complex microbial consortia

10.5194/bg-2017-270 ◽

2017 ◽

Author(s):

Rebecca E. Cooper ◽

Karin Eusterhues ◽

Carl-Eric Wegner ◽

Kai Uwe Totsche ◽

Kirsten Küsel

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Shewanella Oneidensis ◽

Model Organism ◽

Microbial Consortia ◽

Rrna Gene ◽

Natural Environments ◽

Mineral Surfaces ◽

Electron Shuttling ◽

Reducing Conditions

Abstract. The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. In this study we investigated to which extent the content of adsorbed or coprecipitated OM on ferrihydrite influences the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM contents led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella sp. or Geobacter sp., but an enrichment of fermenters (i.e. Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron donor under Fe(III) reducing conditions. In summary, this study shows that increasing concentrations of OM in OM-mineral complexes determines microbial Fe(III) reduction rates and shapes the microbial community structure involved in the reductive dissolution of ferrihydrite. Similarities observed between the complex Fe(III)-reducing microbial consortia and the model Fe(III)-reducer S. oneidensis MR-1 suggest electron shuttling mechanisms dominate in OM-rich environments, including soils, sediments, and fens, where natural OM interacts with Fe(III) oxides during mineral formation.

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Ferrihydrite-associated organic matter (OM) stimulates reduction by <i>Shewanella oneidensis</i> MR-1 and a complex microbial consortia

Biogeosciences ◽

10.5194/bg-14-5171-2017 ◽

2017 ◽

Vol 14 (22) ◽

pp. 5171-5188 ◽

Cited By ~ 20

Author(s):

Rebecca Elizabeth Cooper ◽

Karin Eusterhues ◽

Carl-Eric Wegner ◽

Kai Uwe Totsche ◽

Kirsten Küsel

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Shewanella Oneidensis ◽

Model Organism ◽

Microbial Consortia ◽

Rrna Gene ◽

Natural Environments ◽

Mineral Surfaces ◽

Electron Shuttling ◽

Reducing Conditions

Abstract. The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM–mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM–mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite–OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM–ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM–mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron donor under Fe(III)-reducing conditions. In summary, this study shows that increasing concentrations of OM in OM–mineral complexes determines microbial Fe(III) reduction rates and shapes the microbial community structure involved in the reductive dissolution of ferrihydrite. Similarities observed between the complex Fe(III)-reducing microbial consortia and the model Fe(III)-reducer S. oneidensis MR-1 suggest electron-shuttling mechanisms dominate in OM-rich environments, including soils, sediments, and fens, where natural OM interacts with Fe(III) oxides during mineral formation.

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Quantitative FluorescenceIn SituHybridization Analysis of Microbial Consortia from a Biogenic Gas Field in Alaska's Cook Inlet Basin

Applied and Environmental Microbiology ◽

10.1128/aem.07122-11 ◽

2012 ◽

Vol 78 (10) ◽

pp. 3599-3605 ◽

Cited By ~ 39

Author(s):

Katherine S. Dawson ◽

Dariusz Strąpoć ◽

Brad Huizinga ◽

Ulrika Lidstrom ◽

Matt Ashby ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Microbial Community Composition ◽

Reaction Network ◽

Microbial Consortia ◽

Geochemical Data ◽

Cook Inlet ◽

Gas Field ◽

Content Type ◽

Cook Inlet Basin

ABSTRACTFilter-collected production water samples from a methane-rich gas field in the Cook Inlet basin of Alaska were investigated using whole-cell rRNA-targeted fluorescencein situhybridization (FISH) and 16S rRNA tag pyrosequencing. Both techniques were consistent in determining the microbial community composition, including the archaeal or bacterial dominance of samples. The archaeal community is dominated by the obligate methylotrophic methanogen genusMethanolobusas well as the nutritional generalist methanogen genusMethanosarcina, which is capable of utilizing acetate, CO2, and methyl-bearing compounds. The most-abundant bacterial groups areFirmicutes, notably of theAcetobacteriumgenus, andCytophaga-Flexibacter-Bacteroidesspecies (CFBs) affiliated with the orderBacteroidales. We observed spatial variation among samples in both the percentage of members ofArchaeacompared to that of members ofBacteriaand the dominant members of the bacterial community, differences which could not be explained with the available geochemical data. Based upon the microbial community composition and the isotopic signature of methane associated with the Cook Inlet basin site, we propose a simplified reaction network beginning with the breakdown of coal macromolecules, followed by fermentation and methylotrophic and acetoclastic methane production.

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Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

Microorganisms ◽

10.3390/microorganisms10010071 ◽

2021 ◽

Vol 10 (1) ◽

pp. 71

Author(s):

Xiaofeng Wu ◽

Chijioke O. Elekwachi ◽

Shiping Bai ◽

Yuheng Luo ◽

Keying Zhang ◽

...

Keyword(s):

Microbial Community ◽

Plant Biomass ◽

High Arctic ◽

Glycoside Hydrolases ◽

Microbial Consortia ◽

Biomass Hydrolysis ◽

Host Animal ◽

Ovibos Moschatus ◽

Plant Polysaccharide ◽

Rumen Microbiome

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

Animal Microbiome ◽

10.1186/s42523-021-00126-z ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sally L. Bornbusch ◽

Rachel L. Harris ◽

Nicholas M. Grebe ◽

Kimberly Roche ◽

Kristin Dimac-Stohl ◽

...

Keyword(s):

Antibiotic Resistance ◽

Microbial Community ◽

Gut Microbiota ◽

Microbial Diversity ◽

Community Composition ◽

Microbial Community Composition ◽

Microbial Consortia ◽

Metagenomic Sequencing ◽

Negative Consequences

Abstract Background Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases. Results Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups. Conclusions Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

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Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

10.7287/peerj.preprints.2338v1 ◽

2016 ◽

Author(s):

Tanya Brown ◽

Christopher Otero ◽

Alejandro Grajales ◽

Estefania Rodriguez ◽

Mauricio Rodriguez-Lanetty

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Species ◽

Sea Anemone ◽

Microbial Consortia ◽

Rrna Gene ◽

Core Microbiome ◽

Wide Range ◽

Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

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Mosaic Patterns of B-vitamin Synthesis and Utilization in a Natural Marine Microbial Community

10.1101/280438 ◽

2018 ◽

Author(s):

Laura Gómez-Consarnau ◽

Rohan Sachdeva ◽

Scott M. Gifford ◽

Lynda S. Cutter ◽

Jed A. Fuhrman ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

De Novo ◽

B Vitamins ◽

Microbial Consortia ◽

Vitamin B ◽

Complex Interactions ◽

Spatial Changes ◽

One Year ◽

B Vitamin

Aquatic environments contain diverse microbial communities whose complex interactions mediate the cycling of major and trace nutrients such as vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus their exchange among de-novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural coastal microbial community, diel sampled-quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Our transcriptomic data show that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B12synthesis, but not of vitamin-B7, whose synthesis transcripts were mainly represented by Flavobacteria.In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B1synthesis transcripts. Furthermore, ambient vitamin-B1concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-aconcentration. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature.

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Worldwide exploration of the microbiome harbored by the cnidarian model,Exaiptasia pallida(Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PeerJ ◽

10.7717/peerj.3235 ◽

2017 ◽

Vol 5 ◽

pp. e3235 ◽

Cited By ~ 8

Author(s):

Tanya Brown ◽

Christopher Otero ◽

Alejandro Grajales ◽

Estefania Rodriguez ◽

Mauricio Rodriguez-Lanetty

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Species ◽

Sea Anemone ◽

Microbial Consortia ◽

Rrna Gene ◽

Core Microbiome ◽

Wide Range ◽

Exaiptasia Pallida

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemoneExaiptasia pallidashows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated withE. pallidaare broadly conserved across geographic space with samples, containing largelyProteobacteriaandBacteroides.However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgalSymbiodiniumsymbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact thatE. pallidais likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone modelE. pallidais the first global-scale study of its kind.

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