Microbial community composition and<i>in silico</i>predicted metabolic potential reflect biogeochemical gradients between distinct peatland types

Urbanová, Zuzana; Bárta, Jiří

doi:10.1111/1574-6941.12422

Cited by 36 publications

(23 citation statements)

References 63 publications

(145 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Whereas the Actinobacteria seem to be more or less uniform with regard to their metabolism and ecological requirements, Proteobacteria exhibit many different lifestyles and, therefore, the relative abundance of the main proteobacterial classes also varied between the lake sites. Some members of Proteobacteria are known to utilize easily available substrates quickly, as well as having the ability to use different compounds as electron donors [63].…”

Section: Discussionmentioning

confidence: 99%

Prokaryotic Community Composition Affected by Seasonal Changes in Physicochemical Properties of Water in Peat Bog Lakes

Lew

Glińska-Lewczuk

Ziembińska-Buczyńska

2018

Water

View full text Add to dashboard Cite

Based on a three-year study on the prokaryotic community composition in peat bog lakes surrounded by a floating mat of Sphagnum sp. moss in the conditions of Northeast Poland (Central Europe), we verified the relationship between 20 water parameters and main Eubacteria and Archaea phyla for specific sites: the subsurface (pelagic zone), near-bottom (benthic zone), and the Sphagnum mat (ecotone zone). Abundance and composition of the main aquatic bacteria phyla (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria) and Archaea were associated with different combinations of physico-chemical parameters of water, and followed temporal variations of temperature, dissolved organic carbon (DOC), aromaticity, and water color. Redundancy analysis (RDA) showed that water acidity is a less significant predictor of bacterial activity; however, we have found Betaproteobacteria negatively correlated (r = −0.49, p = 0.01), while Actinobacteria positively correlated (r = 0.21, p = 0.05) to pH. This relation was the most significant in the ecotone zone. In the overall bacteria community structure Betaproteobacteria dominated (18.3%) regardless of site or season, except for winter when, at low temperatures and DOC concentrations, Actinobacteria increased to 22.9%. The Archaea fraction was uniform (11%) in seasons and sites and showed no specific preferences to physico-chemical predictors. Although the water parameters from the Sphagnum mat did not differ significantly from pelagic water, its role as a source of allochthonous organic matter is crucial for bacteria activity. The relations between peat bog lake attributes and seasonal changes in bacterial diversity demonstrated a distinct divergent pattern for each prokaryote. Obtaining results will provide support for any future evaluation of the effects of environmental variables on prokaryotic community structures in peat bog lakes.

show abstract

Section: Discussionmentioning

confidence: 99%

Prokaryotic Community Composition Affected by Seasonal Changes in Physicochemical Properties of Water in Peat Bog Lakes

Lew

Glińska-Lewczuk

Ziembińska-Buczyńska

2018

Water

View full text Add to dashboard Cite

show abstract

“…Next, we categorized the relative importance of KO genes by ranking them according to their counts. These counts were obtained with PICRUSt v.1.1.0 ( Langille et al, 2013 ) and were log transformed to rank their relative abundance ( Urbanová & Bárta, 2014 ). We focused our attention on a chosen subset of KOs with the highest counts ( n = 10 selected at random), as a first order analysis to characterize functional differences between these microbiotas.…”

Section: Methodsmentioning

confidence: 99%

Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico

Cicala

Cisterna-Céliz

Moore

et al. 2018

PeerJ

View full text Add to dashboard Cite

The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.

show abstract

“…Actinobacteria, Bacteroidetes, and Proteobacteria, which dominated here, also tend to dominate other permafrost environments (Yergeau et al, 2010 ; Frank-Fahle et al, 2014 ; Johnston et al, 2016 ), although Deltaproteobacteria and not Alphaproteobacteria or Betaproteobacteria were more abundant in this study. Nitrospirae were found to be abundant in different kinds of Northern wetlands (Wilhelm et al, 2011 ; Urbanová and Bárta, 2014 ). Other studies have also reported Chloroflexi and Cyanobacteria (Ganzert et al, 2014 ; Hultman et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources

et al. 2018

View full text Add to dashboard Cite

Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.

show abstract

Microbial community composition andin silicopredicted metabolic potential reflect biogeochemical gradients between distinct peatland types

Cited by 36 publications

References 63 publications

Prokaryotic Community Composition Affected by Seasonal Changes in Physicochemical Properties of Water in Peat Bog Lakes

Prokaryotic Community Composition Affected by Seasonal Changes in Physicochemical Properties of Water in Peat Bog Lakes

Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico

Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources

Contact Info

Product

Resources

About