Fibrolytic Bacteria Isolated from the Rumen of North American Moose (Alces alces) and Their Use as a Probiotic in Neonatal Lambs

Fibrolytic bacteria were isolated from the rumen of North American moose (Alces alces), which eat a high-fiber diet of woody browse. It was hypothesized that fibrolytic bacteria isolated from the moose rumen could be used as probiotics to improve fiber degradation and animal production. Thirty-one isolates (Bacillus, n = 26; Paenibacillus, n = 1; and Staphylococcus, n = 4) were cultured from moose rumen digesta samples collected in Vermont. Using Sanger sequencing of the 16S rRNA gene, culturing techniques, and optical densities, isolates were identified and screened for biochemical properties important to plant carbohydrate degradation. Five isolates were selected as candidates for use as a probiotic, which was administered daily to neonate lambs for 9 weeks. It was hypothesized that regular administration of a probiotic to improve fibrolysis to neonate animals through weaning would increase the developing rumen bacterial diversity, increase animal production, and allow for long-term colonization of the probiotic species. Neither weight gain nor wool quality was improved in lambs given a probiotic, however, dietary efficiency was increased as evidenced by the reduced feed intake (and rearing costs) without a loss to weight gain. Experimental lambs had a lower acetate to propionate ratio than control lambs, which was previously shown to indicate increased dietary efficiency. Fibrolytic bacteria made up the majority of sequences, mainly Prevotella, Butyrivibrio, and Ruminococcus. While protozoal densities increased over time and were stable, methanogen densities varied greatly in the first six months of life for lambs. This is likely due to the changing diet and bacterial populations in the developing rumen.     

Persistence of host-specific <Emphasis Type="Italic">Bacteroides–Prevotella</Emphasis> 16S rRNA genetic markers in environmental waters: effects of temperature and salinity

Host-specific Bacteroides–Prevotella 16S rRNA genetic markers are promising alternative indicators for identifying the sources of fecal pollution because of their high abundance in the feces of warm-blooded animals and high host specificity. However, little is known about the persistence of these genetic markers in environments after being released into environmental waters. The persistence of feces-derived four different host-specific Bacteroides–Prevotella 16S rRNA genetic makers (total, human-, cow-, and pig-specific) in environmental waters was therefore investigated at different incubation temperatures (4, 10, 20, and 30°C) and salinities (0, 10, 20, and 30 ppt) and then compared with the survival of conventional fecal-indicator organisms. The host-specific genetic markers were monitored by using real-time polymerase chain reaction (PCR) assays with specific primer sets. Each host-specific genetic marker showed similar responses in non-filtered river water and seawater: They persisted longer at lower temperatures and higher salinities. In addition, these markers did not increase in all conditions tested. Decay rates for indicator organisms were lower than those for host-specific genetic markers at temperature above 10°C. Furthermore, we investigated whether the PCR-detectable 16S rRNA genetic markers reflect the presence of live target cells or dead target cells in environmental waters. The result revealed that the detection of the Bacteroides–Prevotella 16S rRNA genetic markers in environmental waters mainly reflected the presence of ‘viable but non-culturable’ Bacteroides–Prevotella cells. These findings indicate that seasonal and geographical variations in persistence of these host-specific Bacteroides–Prevotella 16S rRNA genetic markers must be considered when we use them as alternative fecal indicators in environmental waters.     

Intestinal bacterial population of healthy rats during the administration of chitosan and chitooligosaccharides

The effect of the administration of chitosan (CS) and chitooligosaccharides (COS) on rat fecal microbiota was analyzed in this study. The profile of total bacterial population was monitored during 3 weeks of CS or COS application using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons. Quantitative PCR was used for monitoring possible changes in the levels of total bacteria and the levels of individual bacterial groups: Bifidobacteria, Clostridium leptum, Enterobacteriaceae, Lactobacillus–Streptococcus–Enterobacter, and Bacteroides–Prevotella. The DGGE profiles revealed a high complexity and individuality of each tested subject, and variations in the composition of band pattern were observed. CS or COS per os administration changed the profile and structure of the microbial ecosystem of the gastrointestinal tract of healthy rats. COS have, in most cases, an opposite effect compared with CS; only the Bacteroides–Prevotella bacterial group and Enterobacteriaceae were influenced in the same way. The Bifidobacteria group was not influenced by the administration CS and COS.     

Quantification of host-specific <Emphasis Type="Italic">Bacteroides–Prevotella</Emphasis> 16S rRNA genetic markers for assessment of fecal pollution in freshwater

Based on the comparative 16S rRNA gene sequence analysis of fecal DNAs, we identified one human-, three cow-, and two pig-specific Bacteroides–Prevotella 16S rRNA genetic markers, designed host-specific real-time polymerase chain reaction (real-time PCR) primer sets, and successfully developed real-time PCR assay to quantify the fecal contamination derived from human, cow, and pig in natural river samples. The specificity of each newly designed host-specific primer pair was evaluated on fecal DNAs extracted from these host feces. All three cow-specific and two pig-specific primer sets amplified only target fecal DNAs (in the orders of 9–11 log₁₀ copies per gram of wet feces), showing high host specificity. This real-time PCR assay was then applied to the river water samples with different fecal contamination sources and levels. It was confirmed that this assay could sufficiently discriminate and quantify human, cow, and pig fecal contamination. There was a moderate level of correlation between the Bacteroides–Prevotella group-specific 16S rRNA gene markers with fecal coliforms (r ² = 0.49), whereas no significant correlation was found between the human-specific Bacteroides 16S rRNA gene with total and fecal coliforms. Using a simple filtration method, the minimum detection limits of this assay were in the range of 50–800 copies/100 ml. With a combined sample processing and analysis time of less than 8 h, this real-time PCR assay is useful for monitoring or identifying spatial and temporal distributions of host-specific fecal contaminations in natural water environments.     

A shift towards succinate-producing Prevotella in the ruminal microbiome challenged with monensin

The time-resolved impact of monensin on the active rumen microbiome was studied in a rumen-simulating technique (Rusitec) with metaproteomic and metabolomic approaches. Monensin treatment caused a decreased fibre degradation potential that was observed by the reduced abundance of proteins assigned to fibrolytic bacteria and glycoside hydrolases, sugar transporters and carbohydrate metabolism. Decreased proteolytic activities resulted in reduced amounts of ammonium as well as branched-chain fatty acids. The family Prevotellaceae exhibited increased resilience in the presence of monensin, with a switch of the metabolism from acetate to succinate production. Prevotella species harbour a membrane-bound electron transfer complex, which drives the reduction of fumarate to succinate, which is the substrate for propionate production in the rumen habitat. Besides the increased succinate production, a concomitant depletion of methane concentration was observed upon monensin exposure. Our study demonstrates that Prevotella sp. shifts its metabolism successfully in response to monensin exposure and Prevotellaceae represents the key bacterial family stabilizing the rumen microbiota during exposure to monensin.     

Systematics and evolution of ruminal species of the genus Prevotella

Bacterial species of the genusPrevotella represent a numerically dominant microbial population in the rumen of cattle. They belong to the phylogenetic divisionCytophaga-Flexibacter-Bacteroides (CFB) which is a large group of ecologically diverse bacteria with only a few shared traits. The phylogenetic descent from a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal RNA analysis. Only 4 ruminalPrevotella species have been described to date, even though the sequence analysis of directly retrieved 16S rRNA genes indicates a large genetic diversity within this group of rumen bacteria. The closest relatives of ruminalPrevotella spp. are not surprisingly other species of the genusPrevotella, typically inhabiting the gastrointestinal tract, oral cavity and genital areas of other animals and man. The previous phylogenetic analysis showed that species of the genusPrevotella can be split into two groups or superclusters, the “ruminal” and the “non-ruminal prevotellas”. One of 4 currently described ruminalPrevotella spp.,i.e. P. albensis, has been placed outside the supercluster containing ruminalPrevotella spp. and within the supercluster containing the non-ruminalPrevotella spp. However, the number of available small subunit rRNA sequences from this species represents only a fraction of all known ruminalPrevotella sequences.     

Occurrence of virus-like particles in the Dead Sea

Electron-microscopic examination of water samples from the hypersaline Dead Sea showed the presence of high numbers of virus-like particles. Between 0.9 and 7.3 × 10⁷ virus-like particles ml⁻¹ were enumerated in October 1994 in the upper 20 m of the water column during the decline of a bloom of halophilic Archaea. Virus-like particles outnumbered bacteria by a factor of 0.9–9.5 (average 4.4). A variety of viral morphologies were detected, the most often encountered being spindle-shaped, followed by polyhedral and tailed phages. In addition, other types of particles were frequently found, such as unidentified algal scales, and virus-sized star-shaped particles. Water samples collected during 1995 contained low numbers of both bacteria and virus-like particles (1.9–2.6 × 10⁶ and 0.8–4.6 × 10⁷ ml⁻¹ in April 1995), with viral numbers sharply declining afterwards (less than 10⁴ ml⁻¹ in November 1995–January 1996). It is suggested that viruses may play a major role in the decline of halophilic archaeal communities in the Dead Sea, an environment in which protozoa and other predators are absent. Received: February 5, 1997 / Accepted: May 24, 1997     

Microbial communities in saline lakes of the Vestfold Hills (eastern Antarctica)

A detailed survey was undertaken of the microbial communities of 16 saline lakes in the Vestfold Hills (Princess Elizabeth Land, eastern Antarctica), which ranged in salinity from slightly brackish (4–5‰) to hypersaline (maximum: 174‰). Temperatures at comparable sampling depths in the lakes ranged from −12.2°C to +10.5°C. Ranges in the abundances of bacteria, heterotrophic nanoflagellates (HNAN) and phototrophic nanoflagellates (PNAN) were 1.40 × 10⁷ l⁻¹–1.58 × 10¹⁰ l⁻¹, 4.83 × 10⁴ l⁻¹–1.70 × 10⁷ l⁻¹ and 0–1.02 × 10⁷ l⁻¹, respectively. There was considerable variation across the salinity spectrum, though in the case of bacteria and PNAN significantly higher concentrations of cells were seen in two of the most saline lakes. The autotrophic ciliate Mesodinium rubrum occurred in all but five of the lakes and was found at salinity levels up to 108‰. Heterotrophic ciliates were generally scarce. Dinoflagellates, particularly Gonyaulax c.f. tamarensis, Gyrodinium lachryma and Gymnodinium sp., occurred in the majority of the lakes. On the basis of chlorophyll a concentrations, nutrient levels and microplankton concentrations the lakes spanned the spectrum from ultra-oligotrophic to oligo/mesotrophic. The most saline lakes had much reduced species diversity compared with the less saline environments. Isolation from the marine environment has led to nutrient depletion, simplification and a truncated trophic structure. Received: 19 September 1996 / Accepted: 13 January 1997     

Heterotrophic bacterial and viral dynamics in Arctic freshwaters: results from a field study and nutrient-temperature manipulation experiments

Heterotrophic bacterial and viral concentrations (range, 0.7 × 10⁴ to 206.2 × 10⁴ ml⁻¹ and 0.05 × 10⁶ to 128.9 × 10⁶ ml⁻¹, respectively) were determined in several Arctic freshwater environments, including lakes and glacial ecosystems (78.55°N, 11.56°E). Our bacteria and virus results mirrored trends seen in temperate lakes, with an average virus-to-bacteria ratio (VBR) of 13 (range, 7.3–25.2) and viral concentrations and DOC positively correlated with bacterial concentrations (R = 0.964, P < 0.01 and R = 0.813, P < 0.05, respectively). Lysogenic bacteria, determined by induction with Mitomycin C, were not detected in any of the investigated Arctic freshwater environments. Nutrient-addition experiments at in situ and at elevated temperatures were performed to elucidate the factors which influenced the bacterial growth and the virus–bacteria interactions in Arctic freshwaters. Our results suggest that multiple limiting factors interacted and constrained bacterial growth. Bacterial concentrations and doubling times increased at elevated temperatures and appeared to be co-stimulated by phosphorus and carbon. However, viral concentrations showed a lack of response to nutrient addition thus indicating an uncoupling between bacteria and viruses in the experiment.     

In vitro degradation of wheat straw by anaerobic fungi from small ruminants

Abstract

Anaerobic ruminal fungi may play an active role in fibre degradation as evidenced by the production of different fibrolytic enzymes in culture filtrate. In the present study, 16 anaerobic fungal strains were isolated from ruminal and faecal samples of sheep and goats. Based on their morphological characteristics they were identified as species of Anaeromyces, Orpinomyces, Piromyces and Neocallimastix. Isolated Neocallimastix sp. from goat rumen showed a maximum activity of CMCase (47.9 mIU ml^?1) and filter paper cellulase (48.3 mIU ml^?1), while Anaeromyces sp. from sheep rumen showed a maximum xylanolytic activity (48.3 mIU ml^?1). The cellobiase activity for all the isolates ranged from 178.0 – 182.7 mIU ml^?1. Based on the enzymatic activities, isolated Anaeromyces sp. from sheep rumen and Neocallimastix sp. from goat rumen were selected for their potential of in vitro fibre degradation. The highest in vitro digestibility of NDF (23.2%) and DM (34.4%) was shown for Neocallimastix sp. from goat rumen, as compared to the digestibility of NDF and DM in the control group of 17.5 and 25.0%, respectively.     

Protozoan Bacterivory in the Ice and the Water Column of a Cold Temperate Lagoon

Abstract Bacterial abundance and bacterivorous protist abundance and activity were examined in ice-brine and water column communities of a cold temperate Japanese lagoon (Saroma-Ko Lagoon, Hokkaido, 44°N, 144°E), during the late winter phase of ice community development (February–March 1992). Bacterial abundance averaged 6 and 1 × 10⁵ cells ml⁻¹ in the ice-brine and plankton samples, respectively, and generally decreased during the sampling period. Bacterivorous protists, identified based on direct observation of short-term (<1 h) ingested fluorescently labeled bacteria (FLB) in their food vacuoles, were largely dominated by flagellates, mainly cryothecomonad-type and chrysomonad-like cells and small dinoflagellates of the genus Gymnodinium. Bacterivorous ciliates included mainly the prostomatid Urotricha sp., the scuticociliates Uronema and Cyclidium, the choreotrichs Lohmaniella oviformis and Strobilidium, and the hypotrich Euplotes sp. Protist abundance averaged 4 × 10³ and 8.1 cells ml⁻¹ in the ice-brine and 0.3 × 10³ and 1.2 cells ml⁻¹ in the plankton, for flagellates and ciliates, respectively. In contrast to bacteria, the abundance of protists generally increased throughout the sampling period, indicating predator–prey interactions. Protistan bacterivory, measured from the rate of FLB disappearance over 24 h, averaged 36% (ice) and 24% (plankton) of bacterial standing stock and exhibited the same seasonal pattern as for protist abundance. The calculated specific clearance (range, 2–67 nl protozoa⁻¹ h⁻¹) and ingestion (<1–26 particles protozoa⁻¹ h⁻¹) rates were likely to be minimal estimates and grazing impact may have been higher on occasion. Indications for the dependence of ``bacterivorous protists' on nonbacterial food items were also provided. Although alternative sources of bacterial loss are likely to be of importance, this study provides evidence for the potential of protozoan assemblages as bacterial grazers in both sea ice-brine biota and water column at the southern limit of sea ice in the northern hemisphere. Received: 30 July 1998; Accepted: 18 November 1998     

Characterization of rumen bacterial diversity and fermentation parameters in concentrate fed cattle with and without forage

Aims: To determine the effects of the removal of forage in high‐concentrate diets on rumen fermentation conditions and rumen bacterial populations using culture‐independent methods. Methods and Results: Detectable bacteria and fermentation parameters were measured in the solid and liquid fractions of digesta from cattle fed two dietary treatments, high concentrate (HC) and high concentrate without forage (HCNF). Comparison of rumen fermentation conditions showed that duration of time spent below pH 5·2 and rumen osmolality were higher in the HCNF treatment. Simpson’s index of 16S PCR‐DGGE images showed a greater diversity of dominant species in the HCNF treatment. Real‐time qPCR showed populations of Fibrobacter succinogenes (P = 0·01) were lower in HCNF than HC diets. Ruminococcus spp., F. succinogenes and Selenomonas ruminantium were at higher (P ≤ 0·05) concentrations in the solid vs the liquid fraction of digesta regardless of diet. Conclusions: The detectable bacterial community structure in the rumen is highly diverse. Reducing diet complexity by removing forage increased bacterial diversity despite the associated reduction in ruminal pH being less conducive for fibrolytic bacterial populations. Quantitative PCR showed that removal of forage from the diet resulted in a decline in the density of some, but not all fibrolytic bacterial species examined. Significance and Impact of the Study: Molecular techniques such as DGGE and qPCR provide an increased understanding of the impacts of dietary changes on the nature of rumen bacterial populations, and conclusions derived using these techniques may not match those previously derived using traditional laboratory culturing techniques.     

Microbial communities of the stratified soda Lake Doroninskoe (Transbaikal region)

The physicochemical properties, species composition, and vertical distribution of microorganisms in the water column, shoreline microbial mat, and small shoreline mud volcanoes of the stratified soda Lake Doroninskoe were investigated in September 2007. The lake is located in the Transbaikal region, in the permafrost zone (51°25′N; 112°28′E). The maximal depth of the contemporary lake is about 6 m, the pH value of the water is 9.72, and the water mineralization in the near-bottom horizon is 32.3 g l⁻¹. In summer, the surface oxygen-containing horizon of the water column becomes demineralized to 26.5 g l⁻¹; at a depth of 3.5–4.0 m, an abrupt transition occurs to the aerobic zone containing hydrosulfide (up to 12.56 g l⁻¹). Hydrosulfide was also detected in trace quantities in the upper water horizons. The density stratification of the water column usually ensures stable anaerobic conditions until the freezing period (November and December). The primary production of oxygenic phototrophs reached 176–230 μg l⁻¹. High rates of dark CO₂ assimilation (61–240 μg l⁻¹) were detected in the chemocline. Within this zone, an alkaliphilic species of sulfur-oxidizing bacteria of the genus Thioalkalivibrio was detected (10⁴ cells ml⁻¹). Lithoheterotrophic bacteria Halomonas spp., as well as bacteriochlorophyll a-containing aerobic anoxygenic phototrophic bacteria (AAP) Roseinatronobacter sp. capable of thiosulfate oxidation, were isolated from samples collected from the aerobic zone (0–3 m). The water transparency in September was extremely low; therefore, no visible clusters of anoxygenic phototrophic bacteria (APBs) were detected at the boundary of the hydrosulfide layer. However, purple sulfur bacteria which, according to the results of the 16S rRNA gene analysis, belong to the species Thioalkalicoccus limnaeus, Ectothiorhodospira variabilis, “Ect. magna,” and Ect. shaposhnikovii, were isolated from samples of deep silt sediments. Ect. variabilis and Ect. shaposhnikovii were the major APB species in the shoreline algo-bacterial mat. The halotolerant bacterium Ect. shaposhnikovii, purple nonsulfur bacteria of the genus Rhodobacter, and AAP of Roseococcus sp. were isolated from the samples collected from mud volcanoes. All these species are alkaliphiles, moderate halophiles, or halotolerant microorganisms.     

Proteinase Activity of Prevotella Species Associated with Oral Purulent Infection

Prevotella intermedia and Prevotella nigrescens are often regarded as principal causes of acute dentoalveolar infection; however, other species within the genus are also known to be associated with such infection. The aim of this study was to determine the in vitro proteolytic activity of these different Prevotella species that have been implicated with dentoalveolar infection. A total of 234 strains were obtained from pus specimens from dentoalveolar infection and from the plaque of healthy volunteers. Prevotella loescheii, Prevotella oralis, Prevotella melaninogenica, Prevotella buccae, and Prevotella denticola were all shown to have a proteolytic activity (8.5–10.5 × 10⁻⁸ A-units) lower than that of P. intermedia and P. nigrescens (21.1–23.5 × 10⁻⁸ A-units). In the case of P. loescheii, P. melaninogenica, and P. intermedia, the level of proteolytic activity for clinical strains was significantly (P < 0.05) higher than that recorded for commensal strains. Proteolytic activity for all species of Prevotella examined was inhibited by N-ethylmaleimide and phenymethylsulfonyl fluoride. This study suggests that Prevotella species associated with oral purulent infection produce cysteine and serine proteinases and that in certain species of Prevotella, the strains involved in infection exhibit higher proteolytic activity when compared with strains from healthy sites.     

Preliminary observations on the concentration of marine bacteriophages in the water around Helgoland

In a preliminary survey, conducted between August 28 and October 9, 1990, the concentration of bacteriophages in seawater sampled at intervals of 1 to 4 days near Helgoland (station Kabeltonne) was determined by using indicator bacteria which had been isolated from seawater sampled only some weeks before. With a number of bacterial strains, phage concentrations ranging between 2 and 7×10²ml⁻¹ were found. However, during the course of this investigation maximal concentrations lasted for a few days only. With most indicator bacteria employed, the concentration of plaque-forming units (PFU) varied in the range of <1 and 20–30 PFU ml⁻¹.     

Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community,Composition, and Diversity in Yanbian Yellow Cattle

The rumen microbial ecosystem is a complex system where rumen fermentation processes involve interactions among microorganisms. There are important relationships between diet and the ruminal bacterial composition. Thus, we investigated the ruminal fermentation characteristics and compared ruminal bacterial communities using tag amplicon pyrosequencing analysis in Yanbian yellow steers, which were fed linseed oil (LO) and propionate precursors. We used eight ruminally cannulated Yanbian yellow steers (510 ± 5.8 kg) in a replicated 4 × 4 Latin square design with four dietary treatments. Steers were fed a basal diet that comprised 80% concentrate and 20% rice straw (DM basis, CON). The CON diet was supplemented with LO at 4%. The LO diet was also supplemented with 2% dl-malate or 2% fumarate as ruminal precursors of propionate. Dietary supplementation with LO and propionate precursors increased ruminal pH, total volatile fatty acid concentrations, and the molar proportion of propionate. The most abundant bacterial operational taxonomic units in the rumen were related to dietary treatments. Bacteroidetes dominated the ruminal bacterial community and the genus Prevotella was highly represented when steers were fed LO plus propionate precursors. However, with the CON and LO diet plus malate or fumarate, Firmicutes was the most abundant phylum and the genus Ruminococcus was predominant. In summary, supplementing the diets of ruminants with a moderate level of LO plus propionate precursors modified the ruminal fermentation pattern. The most positive responses to LO and propionate precursors supplementation were in the phyla Bacteriodetes and Firmicutes, and in the genus Ruminococcus and Prevotella. Thus, diets containing LO plus malate or fumarate have significant effects on the composition of the rumen microbial community.     

Quantitative Determination of H2-Utilizing Acetogenic and Sulfate-Reducing Bacteria and Methanogenic Archaea from Digestive Tract of Different Mammals

Total number of bacteria, cellulolytic bacteria, and H₂-utilizing microbial populations (methanogenic archaea, acetogenic and sulfate-reducing bacteria) were enumerated in fresh rumen samples from sheep, cattle, buffaloes, deer, llamas, and caecal samples from horses. Methanogens and sulfate reducers were found in all samples, whereas acetogens were not detected in some samples of each animal. Archaea methanogens were the largest H₂-utilizing populations in all animals, and a correlation was observed between the numbers of methanogens and those of cellulolytic microorganisms. Higher counts of acetogens were found in horses and llamas (1 × 10⁴ and 4 × 10⁴ cells ml⁻¹ respectively).     

Effects of water velocity on picoplankton uptake by coral reef communities

In previous experiments, rates of picoplankton uptake into coral communities were controlled by sponge and ascidian biomass. Those experimental communities, however, had relatively few sponges and ascidians. In contrast, turbulent transport of particles into the momentum boundary layers can limit particle removal by layered, dense bivalve populations. In this study, the role of water velocity in controlling particulate nutrient-uptake by rubble communities was evaluated, in which the rubble was more completely covered by sponges and ascidians. Picoplankton uptake was proportional to concentration over a range of cell concentrations from 3.0 × 10⁵ to 9.5 × 10⁵ heterotrophic bacteria ml⁻¹, 4.1 × 10⁴ to 1.2 × 10⁵ Synechococcus sp. ml⁻¹ and 6.3 × 10³ to 1.8 × 10⁴ picoeukaryotes ml⁻¹. The first-order uptake rate constants, normalized to sponge and ascidian biomass, were similar to previous experimental communities. Picoplankton uptake increased 1.6-fold over a 7-fold change in water velocity, 0.05–0.35 m s⁻¹. This increase has been interpreted as a result of higher turbulent transport within the rough coral community (canopy), as indicated by a 1.6-fold increase in the bottom friction with increasing water velocity.     

Phylogenetic composition of bacterial communities in small boreal lakes and ombrotrophic bogs of the upper Volga basin

Fluorescent in situ hybridization (FISH) with rRNA-specific oligonucleotide probes was used to assess the numbers and phylogenetic diversity of prokaryotic microorganisms in the water of small boreal lakes and peatland catchments of the swampy upper Volga basin. The abundance of bacterioplankton in lake water was found to vary from 1.6 to 8.7 × 10⁶ cells ml⁻¹, with the highest values detected in neutral eutrophic lakes. The total cell numbers in the peat of ombrotrophic bogs were 3.9–4.3 × 10⁸ cells g⁻¹ of wet peat. The proportion of bacteria identified by the group-specific probes decreased from 79–85% in neutral (pH 6.6–6.9) mesotrophic and eutrophic lakes to 65–69% in acidic (pH 4.4–5.5) dystrophic lakes and to 51–58% in the peat of acidic (pH 3.6–3.9) ombrotrophic bogs. The diversity of bacterial communities was highest in lakes with neutral water. These communities were dominated by members of the phylum Actinobacteria (31–44% of the total bacterial number), while the contribution of Alphaproteobacteria (16–19%), Bacteroidetes (6–16%), Betaproteobacteria (6–7%), Planctomycetes (2–8%), and Gammaproteobacteria (4–5%) was also significant. In acidic dystrophic lakes, Actinobacteria (25–35%) and Betaproteobacteria (25–34%) predominated, while peatland catchments were dominated by the Alphaproteobacteria (20–23%). The presence of acidobacteria and some planctomycetes common for bogs in the water of acidic dystrophic lakes, as well as the high proportion of bacteria (31–49%) that were not identified by the group-specific probes, suggest the impact of microbial processes in peatland catchments on the microbial composition of the receiving waters.