Structure and Function of Microbial Communities

Stahl, David A.; Flowers, Jason J.; Hullar, Meredith A.J.; Davidson, Scott

doi:10.1007/978-3-642-30123-0_34

Cited by 10 publications

(9 citation statements)

References 347 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, other researchers who have studied the microbial consortia of rivers have concluded that river microbes generally are comparable to lake consortia [ 17 , 48 , 49 ]and we expected similar results. In addition, we expected to observe a number of sequences that reflected a “Microbial Loop” [ 50 ] as illustrated for another aquatic system [ 51 ], dominated by heterotrophic bacteria and including representatives of cyanobacteria and algae, protozoans, zooplankton (especially nematodes and cladocerans), insects, and vertebrates. Indeed, both of these expectations were supported, and we observed that approximately half of the most abundant read assignments corresponded to microbes identified as ecologically significant in lakes [ 23 ], fit the expected microbial functional patterns [ 50 ], and corresponded to the major groups of freshwater microbes previously described and summarized [ 24 ] namely: ultramicrobacteria (made up of three groups Polynucleobacter and other Betaproteobacteria , acI Actinobacteria , and certain Alphaproteobacteria ), opportunistic heterotrophs, phototrophs, and filamentous bacteria.…”

Section: Additional Resultsmentioning

confidence: 99%

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Brown

LePrell

Franklin

et al. 2015

Stand in Genomic Sci

View full text Add to dashboard Cite

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 106 reads revealed >3 × 106 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 106 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and ‘Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

show abstract

Section: Additional Resultsmentioning

confidence: 99%

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Brown

LePrell

Franklin

et al. 2015

Stand in Genomic Sci

View full text Add to dashboard Cite

show abstract

“…Microbial mats are intricately organized structures that provide functional advantage to their inhabitants (e.g., Stahl et al, 2013 ). Mat architecture reflects both ecology and physiology in that it promotes the metabolisms of the microbes that construct the mat.…”

Section: Introductionmentioning

confidence: 99%

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

et al. 2016

View full text Add to dashboard Cite

Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history.

show abstract

“…Although schematic models commonly depict cycles of individual elements, e.g., the carbon cycle, processes affecting the cycling of one element commonly also affect the cycling of other elements (Jelen et al, 2016). By driving the biotransformation of elements via their highly diverse and complex enzymatic machineries, biota, especially prokaryotic microbiota, are central to element cycling on Earth (Banfield et al, 2005;Stahl et al, 2013;Paul, 2014). During their >3500 Ma evolution, prokaryotes have developed genetic, physiological, metabolic and ecological capabilities, which allow them to live anywhere where water is available and ambient temperatures are below 121 ºC (Gogarten et al, 2002;Ramette and Tiedje, 2007).…”

Section: Introductionmentioning

confidence: 99%

Cycling of biogenic elements drives biogeochemical gold cycling

Sanyal

Shuster

Reith

2019

Earth-Science Reviews

View full text Add to dashboard Cite

Immediately via their non-commercial personal homepage or blog  by updating a preprint in arXiv or RePEc with the accepted manuscript  via their research institute or institutional repository for internal institutional uses or as part of an invitation-only research collaboration work-group  directly by providing copies to their students or to research collaborators for their personal use  for private scholarly sharing as part of an invitation-only work group on commercial sites with which Elsevier has an agreement After the embargo period via non-commercial hosting platforms such as their institutional repository  via commercial sites with which Elsevier has an agreementIn all cases accepted manuscripts should: link to the formal publication via its DOI  bear a CC-BY-NC-ND licensethis is easy to do  if aggregated with other manuscripts, for example in a repository or other site, be shared in

show abstract

Structure and Function of Microbial Communities

Cited by 10 publications

References 347 publications

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

Cycling of biogenic elements drives biogeochemical gold cycling

Contact Info

Product

Resources

About