Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades

Uz, İlker; Ogram, Andrew

doi:10.1111/j.1574-6941.2006.00120.x

Cited by 27 publications

(32 citation statements)

References 43 publications

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“…Clostridiaceae in the oligotrophic peat, including the two most abundant 13 C-enriched OTUs (Otu2 and Otu4), had high sequence similarities to several acid-tolerant and sugar-fermenting Clostridium species (Tables S4 and S5). In the mesotrophic peat, the two most abundant Clostridium OTUs (Otu1 and Otu3) showed similarities of 99 to 100% to uncultured clostridia from wetland soils (26,28,35,36). Both oligotrophic and mesotrophic peat showed Veillonellaceae OTUs similar to genera Pelosinus, Propionispira, and Psychrosinus (Table S4), but several additional Veillonellaceae OTUs from the mesotrophic peat had no close matches to described species.…”

Section: Resultsmentioning

confidence: 99%

“…These included Clostridiaceae, which are well-known saccharolytic and cellulolytic fermenters and have been suggested to represent important fermenters in acidic peat (26,28,33,36). Another major group of Firmicutes was Veillonellaceae, which have Gram-negative cell walls and have so far been rarely detected in peat or soil habitats, although they have been actively involved in rice straw degradation (63) and detected as minor peat taxa (33,66).…”

Section: Discussionmentioning

confidence: 99%

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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios

Juottonen

Eiler

Biasi

et al. 2017

Appl Environ Microbiol

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Northern peatlands in general have high methane (CH 4 ) emissions, but individual peatlands show considerable variation as CH 4 sources. Particularly in nutrient-poor peatlands, CH 4 production can be low and exceeded by carbon dioxide (CO 2 ) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO 2 to CH 4 produced. After [ 13 C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH 4 and CO 2 . The oligotrophic fen had lower CH 4 production but produced 3 to 59 times more CO 2 than CH 4 . RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH 4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria. The oligotrophic peat with excess CO 2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia. Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH 4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO 2 production in peatlands.IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH 4 ), yet in many peatlands, CO 2 production from unresolved anaerobic processes exceeds CH 4 production. Anaerobic degradation produces the precursors of CH 4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH 4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH 4 production, while novel and unconventional degraders could be identified in a site where CO 2 production greatly exceeds CH 4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH 4 production and reveal bacteria potentially producing the excess CO 2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH 4 emission from peatlands.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios

Juottonen

Eiler

Biasi

et al. 2017

Appl Environ Microbiol

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“…In bighead carp, Clostridium sensu stricto (cluster I), Clostridium XI and Proteocatella were the most abundant Firmicutes. Both Clostridium XlVa and XlVb are versatile in their ability to utilise various polysaccharides, such as cellulose, xylan and hemicelluloses, which constitute the major part of vegetalfibres [45,46]. By contrast, members of the genera Clostridium sensu stricto (cluster I) and Clostridium XI include not only species with saccharolytic and fibre-fermenting activities but also proteolytic species [47,48].…”

Section: −3mentioning

confidence: 99%

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

et al. 2014

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Gut microbiota is increasingly regarded as an integral component of the host, due to important roles in the modulation of the immune system, the proliferation of the intestinal epithelium and the regulation of the dietary energy intake. Understanding the factors that influence the composition of these microbial communities is essential to health management, and the application to aquatic animals still requires basic investigation. In this study, we compared the bacterial communities harboured in the intestines and in the rearing water of grass carp (Ctenopharyngodon idellus), crucian carp (Carassius cuvieri), and bighead carp (Hypophthalmichthys nobilis), by using 454-pyrosequencing with barcoded primers targeting the V4 to V5 regions of the bacterial 16S rRNA gene. The specimens of the three species were cohabiting in the same pond. Between 6,218 and 10,220 effective sequences were read from each sample, resulting in a total of 110,398 sequences for 13 samples from gut microbiota and pond water. In general, the microbial communities of the three carps were dominated by Fusobacteria, Firmicutes, Proteobacteria and Bacteroidetes, but the abundance of each phylum was significantly different between species. At the genus level, the overwhelming group was Cetobacterium (97.29±0.46 %) in crucian carp, while its abundance averaged c. 40 and 60 % of the sequences read in the other two species. There was higher microbial diversity in the gut of filterfeeding bighead carp than the gut of the two other species, with grazing feeding habits. The composition of intestine microbiota of grass carp and crucian carp shared higher similarity when compared with bighead carp. The principal coordinates analysis (PCoA) with the weighted UniFrac distance and the heatmap analysis suggested that gut microbiota was not a simple reflection of the microbial community in the local habitat but resulted from species-specific selective pressures, possibly dependent on behavioural, immune and metabolic characteristics.

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“…These enzymes are among those that produce the monomers and oligomers used by fermenters in anaerobic environments, with the end products of fermentation used as substrates for methanogenesis (Megonigal et al, 2004). In other wetlands, glucosidase activity was also positively correlated with CH 4 production (Morrissey et al, 2013;Freeman et al, 1997), likely because the amount of substrate available for fermentation indirectly affects the amount of substrate available for methanogenesis (Uz and Ogram, 2006). If glucosidase and cellobiosidase are indicative of the quantity of their associated substrate (cellulose), the composition of organic matter must also be important in determining the rate of CH 4 production.…”

Section: Soil Carbon Mineralizationmentioning

confidence: 99%

Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon

2013

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Abstract. Environmental perturbations in wetlands affect the integrated plant-microbial-soil system, causing biogeochemical responses that can manifest at local to global scales. The objective of this study was to determine how saltwater intrusion affects carbon mineralization and greenhouse gas production in coastal wetlands. Working with tidal freshwater marsh soils that had experienced ∼ 3.5 yr of in situ saltwater additions, we quantified changes in soil properties, measured extracellular enzyme activity associated with organic matter breakdown, and determined potential rates of anaerobic carbon dioxide (CO 2 ) and methane (CH 4 ) production. Soils from the field plots treated with brackish water had lower carbon content and higher C : N ratios than soils from freshwater plots, indicating that saltwater intrusion reduced carbon availability and increased organic matter recalcitrance. This was reflected in reduced activities of enzymes associated with the hydrolysis of cellulose and the oxidation of lignin, leading to reduced rates of soil CO 2 and CH 4 production. The effects of long-term saltwater additions contrasted with the effects of short-term exposure to brackish water during three-day laboratory incubations, which increased rates of CO 2 production but lowered rates of CH 4 production. Collectively, our data suggest that the long-term effect of saltwater intrusion on soil CO 2 production is indirect, mediated through the effects of elevated salinity on the quantity and quality of autochthonous organic matter inputs to the soil. In contrast, salinity, organic matter content, and enzyme activities directly influence CH 4 production. Our analyses demonstrate that saltwater intrusion into tidal freshwater marshes affects the entire process of carbon mineralization, from the availability of organic carbon through its terminal metabolism to CO 2 and/or CH 4 , and illustrate that long-term shifts in biogeochemical functioning are not necessarily consistent with short-term disturbance-type responses.

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Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades

Cited by 27 publications

References 43 publications

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon

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Cellulolytic and fermentative guilds in eutrophic soils of the Florida Everglades

Cited by 27 publications

References 43 publications

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO 2 /CH 4 Production Ratios

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO 2 /CH 4 Production Ratios

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon

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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO ₂ /CH ₄ Production Ratios