Abundance Of Phylotypes Research Articles

Nocardioides, Sediminibacterium, Aquabacterium, Variovorax, and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation.

Vinyl chloride (VC) is a frequent groundwater contaminant and a known human carcinogen. Bioremediation is a potential cleanup strategy for contaminated sites; however, little is known about the bacteria responsible for aerobic VC degradation in mixed microbial communities. In attempts to address this knowledge gap, the microorganisms able to assimilate labeled carbon ((13)C) from VC within a mixed culture capable of rapid VC degradation (120μmol in 7days) were identified using stable isotope probing (SIP). For this, at two time points during VC degradation (days 3 and 7), DNA was extracted from replicate cultures initially supplied with labeled or unlabeled VC. The extracted DNA was ultracentrifuged, fractioned, and the fractions of greater buoyant density (heavy fractions, 1.758 to 1.780gmL(-1)) were subject to high-throughput sequencing. Following this, specific primers were designed for the most abundant phylotypes in the heavy fractions. Then, quantitative PCR (qPCR) was used across the buoyant density gradient to confirm label uptake by these phylotypes. From qPCR and/or sequencing data, five phylotypes were found to be dominant in the heavy fractions, including Nocardioides (∼40%), Sediminibacterium (∼25%), Aquabacterium (∼17%), Variovorax (∼6%), and Pseudomonas (∼1%). The abundance of two functional genes (etnC and etnE) associated with VC degradation was also investigated in the SIP fractions. Peak shifts of etnC and etnE gene abundance toward heavier fractions were observed, indicating uptake of (13)C into the microorganisms harboring these genes. Analysis of the total microbial community indicated a significant dominance of Nocardioides over the other label-enriched phylotypes. Overall, the data indicate Nocardioides is primarily responsible for VC degradation in this mixed culture, with the other putative VC degraders generating a small growth benefit from VC degradation. The specific primers designed toward the putative VC degraders may be of use for investigating VC degradation potential at contaminated sites.

New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions

Analyses on bacterial, archaeal communities at family level and methane-production metabolism were conducted in thirteen full-scale and pilot-scale anaerobic sludge digesters. These digesters were operated at different conditions regarding solids concentration, sludge retention time, organic loading rate and feedstock composition, seeking to optimize digester capacity. Correlations between process parameters and identified microbial phylotypes were evaluated based on relative abundance of these phylotypes determined by Quantitative PCR and 16S rDNA amplicon sequencing. Results showed that, Total Solids concentration (TS), among the evaluated operational parameters, demonstrated the most positive correlation with chemical parameters (including NH3 and VFAs) and significant impact on the abundance of key microbial phylotypes regardless of other factors. Digesters were grouped into ‘Higher-TS’ with higher stress (TS > 44 g/L, NH3 > 90 mg/L, VFAs > 300 mg/L) and ‘Lower-TS’ under easier status (TS ≤ 44 g/L, NH3 < 120 mg/L, VFAs < 525 mg/L) in this study. We identified the key microbial phylotypes, i.e. the most abundant and discriminating populations, in ‘Higher-TS’ digesters with high biogas production rate, which were the class Clostridia, the family Methanosarcinaceae and the order Methanobacteriales. Thermoanaerobacteraceae and Syntrophomonadaceae were identified as key families of Clostridia. Methane was produced both from acetoclastic and hydrogenotrophic methanogenesis. By contrast, in ‘Higher-TS’ digesters with low biogas production rate, the classes Alpha-, Beta- and Gamma-proteobacteria were detected in higher percentages, of which Rhodobacteraceae, Comamonadaceae and Xanthomonadaceae were the most abundant families respectively, and Methanomicrobiales was the prevailing methanogen order. Consistently, hydrogenotrophic pathway was predominant for methanogenesis, indicating existence of syntrophic acetate oxidation in such ‘high-stress’, low biogas production rate digesters. These microbial phylotypes were therefore considered to be associated to ‘Higher-TS’ operation. In ‘Lower-TS’ digesters, the abundance of the class Delta-proteobacteria, the families Anaerolineaceae, Rikenellaceae, Candidatus Cloacamonas and Methanosaetaceae was obviously higher compared with those in ‘Higher-TS’ digesters, which were thus considered to be marker phylotypes of easy status. The influence of TS and NH3 on the microbiome should be considered when a ‘TS-increasing’ strategy is applied to increase digester capacity.

Selenite Reduction by Anaerobic Microbial Aggregates: Microbial Community Structure, and Proteins Associated to the Produced Selenium Spheres.

Certain types of anaerobic granular sludge, which consists of microbial aggregates, can reduce selenium oxyanions. To envisage strategies for removing those oxyanions from wastewater and recovering the produced elemental selenium (Se0), insights into the microbial community structure and synthesis of Se0 within these microbial aggregates are required. High-throughput sequencing showed that Veillonellaceae (c.a. 20%) and Pseudomonadaceae (c.a.10%) were the most abundant microbial phylotypes in selenite reducing microbial aggregates. The majority of the Pseudomonadaceae sequences were affiliated to the genus Pseudomonas. A distinct outer layer (∼200 μm) of selenium deposits indicated that bioreduction occurred in the outer zone of the microbial aggregates. In that outer layer, SEM analysis showed abundant intracellular and extracellular Se0 (nano)spheres, with some cells having high numbers of intracellular Se0 spheres. Electron tomography showed that microbial cells can harbor a single large intracellular sphere that stretches the cell body. The Se0 spheres produced by the microorganisms were capped with organic material. X-ray photoelectron spectroscopy (XPS) analysis of extracted Se0 spheres, combined with a mathematical approach to analyzing XPS spectra from biological origin, indicated that proteins and lipids were components of the capping material associated to the Se0 spheres. The most abundant proteins associated to the spheres were identified by proteomic analysis. Most of the proteins or peptide sequences capping the Se0 spheres were identified as periplasmic outer membrane porins and as the cytoplasmic elongation factor Tu protein, suggesting an intracellular formation of the Se0 spheres. In view of these and previous findings, a schematic model for the synthesis of Se0 spheres by the microorganisms inhabiting the granular sludge is proposed.

Changes in the composition of native root arbuscular mycorrhizal fungal communities during a short-term cover crop-maize succession

Arbuscular mycorrhizal fungi (AMF) establish mutualistic associations with the most important agricultural food and feed crops, sustaining plant growth, nutrient uptake and tolerance of biotic and abiotic stresses. Scanty information is available on the role played by crop identity and diversity as a driving force shaping AMF species communities in the field, in particular in low-input and organic farming, where crop rotation and the use of cover crops are common practices. Here, using a molecular approach, we investigated whether plant communities established in low and high diversity cover crop treatments affect the composition of native AMF root communities of subsequent maize in a Mediterranean organic agroecosystem. A total of 16 AMF sequence types were detected, with Acaulospora cavernata as the most abundant phylotype, accounting for 37.4 % of the sequences, followed by Funneliformis mosseae, Claroideoglomus lamellosum and Rhizoglomus intraradices. Sequences matching to Funneliformis caledonium, Diversispora aurantia, Diversispora epigaea and Archaeospora schenckii corresponded to less than 2.0 % of the total. The most abundant sequences retrieved in plants from cover crop treatments were represented by A. cavernata, while sequences in maize roots were related to F. mosseae, R. intraradices and Glomus sp. Such data show for the first time a change in the composition of native AMF communities colonizing maize roots, which was independent of the identity and diversity of the preceding crop. Our findings suggest that host preference may represent a strong driver of AMF community dynamics in agroecosystems, differentially boosting or depressing AMF species, possibly in relation to their functional significance.

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere.

The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice.

Longitudinal variability of diazotroph abundances in the subtropical North Atlantic Ocean

Diazotrophy-related studies in the North Atlantic have largely focused on its western tropical area, leaving the subtropics and the east undersampled. We studied the longitudinal distribution of Trichodesmium, UCYN-A, UCYN-B, the putative Gammaproteobacterium g-24774A11 and Richelia (Het1) along 24.5 degrees N, using quantitative polymerase chain reaction on different size fractions (10, 10-3 and 3-0.2 mm) and additional filament counts for Trichodesmium. Trichodesmium was the most abundant phylotype, followed by UCYN-A, gamma-24774A11 and Het1, with maximum abundances of 8.8 x 10(5), 2.0 x 10(5), 3.3 x 10(3) and 3.4 x 10(2) nifH copies L-1, respectively, whereas UCYN-B was mostly undetected. A clear shift in the diazotroph community was observed at similar to 30 degrees W, coinciding with the transition between the North Atlantic Subtropical Gyre boundary and inner core. This transition zone divided the transect into an eastern half dominated by UCYN-A and western half dominated by Trichodesmium and gamma-24774A11. gamma-24774A11 was only detected in the 10-3 mu m fraction, suggesting their association with larger microbes or aggregates. Our results indicate that typical size fractionation by 10 mu m is not optimal for reconciling diazotroph phylotypes to N-2 fixation rates and that non-cyanobacterial diazotrophs may contribute importantly to bulk diazotrophic activity in the western subtropical North Atlantic.

Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing

Studies of Antarctic eukaryotes have been hampered by their morphological conservatism, small size and the logistical constraints of remote field work, resulting in a deficiency of baseline biodiversity information about Antarctic terrestrial environments. The application of high throughput sequencing (HTS) in metataxonomic approaches is a promising alternative. Here, we apply such HTS approaches to the hitherto largely unsurveyed micro-eukaryote fauna of the Prince Charles Mountains, East Antarctica. We sequenced 18S rDNA amplicons of twelve Antarctic bulk-soil DNA extracts, retrieved from three sampling regions (four bulk-soil extracts per sampling region). After isolating eukaryotic phylotypes with a stringent filtering approach and initial network visualization, we firstly used rarefied data to compare four α diversity metrics between the three regions. Weighted and unweighted inter-sample UniFrac distances were then used for β diversity comparisons among rarefied data. Furthermore, we analysed the distribution of the most abundant phylotypes and phylotype groups. Lastly, we checked the validity of species-level taxonomic assignments using different sets of reference data in conjunction with two different taxonomy assignment approaches. Phylotype numbers in un-rarefied data compared across regions were lowest for Mount Menzies (73°S; 3330 m), intermediate at Mawson Escarpment (73°S; 807 m) and highest at Lake Terrasovoje (70°S; 173 m), likely due to low biological load at the higher latitude and elevation inland sites. Analysis of rarefied data was difficult due to low sequence coverage particularly from Mount Menzies, but indicated differences in Shannon diversity between Mawson Escarpment and Lake Terrasovoje. PCoA of weighted UniFrac distances between samples from Mawson Escarpment and Lake Terrasovoje indicated changes in community composition in relation to elevation of the sampling locations. The most widespread phylotypes were fungal, followed by non-algal protists. Species-level assignments included known Antarctic taxa in all sampling regions. We show that HTS can provide a rapid survey of the micro-eukaryote fauna to provide baseline biodiversity information for remote, harsh, and hitherto largely unsurveyed environments in the Prince Charles Mountains.

Archaea and Bacteria Acclimate to High Total Ammonia in a Methanogenic Reactor Treating Swine Waste.

Inhibition by ammonium at concentrations above 1000 mgN/L is known to harm the methanogenesis phase of anaerobic digestion. We anaerobically digested swine waste and achieved steady state COD-removal efficiency of around 52% with no fatty-acid or H2 accumulation. As the anaerobic microbial community adapted to the gradual increase of total ammonia-N (NH3-N) from 890 ± 295 to 2040 ± 30 mg/L, the Bacterial and Archaeal communities became less diverse. Phylotypes most closely related to hydrogenotrophic Methanoculleus (36.4%) and Methanobrevibacter (11.6%), along with acetoclastic Methanosaeta (29.3%), became the most abundant Archaeal sequences during acclimation. This was accompanied by a sharp increase in the relative abundances of phylotypes most closely related to acetogens and fatty-acid producers (Clostridium, Coprococcus, and Sphaerochaeta) and syntrophic fatty-acid Bacteria (Syntrophomonas, Clostridium, Clostridiaceae species, and Cloacamonaceae species) that have metabolic capabilities for butyrate and propionate fermentation, as well as for reverse acetogenesis. Our results provide evidence countering a prevailing theory that acetoclastic methanogens are selectively inhibited when the total ammonia-N concentration is greater than ~1000 mgN/L. Instead, acetoclastic and hydrogenotrophic methanogens coexisted in the presence of total ammonia-N of ~2000 mgN/L by establishing syntrophic relationships with fatty-acid fermenters, as well as homoacetogens able to carry out forward and reverse acetogenesis.

Different substrates and starter inocula govern microbial community structures in biogas reactors

ABSTRACTThe influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

Nitrogenase expression in estuarine bacterioplankton influenced by organic carbon and availability of oxygen.

The genetic capacity to fix gaseous nitrogen (N) is distributed among diverse diazotrophs belonging to the Bacteria and Archaea. However, only a subset of the putative diazotrophs present actively fix N at any given time in the environment. We experimentally tested whether the availability of carbon and inhibition by oxygen constrain N fixation by diazotrophs in coastal seawater. The goal was to test whether by alleviating these constraints an increased overlap between nitrogenase (nifH)-gene-carrying and -expressing organisms could be achieved. We incubated water from a eutrophic but N-limited fjord in Denmark under high-carbon/low-oxygen conditions and determined bacterial growth and production, diazotrophic community composition (Illumina nifH amplicon sequencing), and nifH gene abundance and expression [quantitative PCR (qPCR) and quantitative reverse transcriptase PCR (qRT-PCR)]. Bacterial abundances and production increased under high-carbon/low-oxygen conditions as did the similarity between present and active diazotrophic communities. This was caused by the loss of specific abundant yet non-active gammaproteobacterial phylotypes and increased expression by others. The prominent active gamma- and epsilonproteobacterial diazotrophs did not, however, respond to these conditions in a uniform way, highlighting the difficulty to assess how a change in environmental conditions may affect a diverse indigenous diazotrophic community.

A comparison of bacterial community structure in seawater pond with shrimp, crab, and shellfish cultures and in non-cultured pond in Ganyu, Eastern China

The aim of this study was to gain an understanding of the effects of mariculture on the bacterial communities in a co-culture pond, which is a popular culture model for shrimp, crab, and shellfish along the eastern coast of China. Six seawater samples were collected from a pond with cultures of shrimp, crab, and shellfish, and six other samples were collected from a non-cultured pond (control). The diversity of the bacterial communities in the samples was examined using the MiSeq desktop sequencer (Illumina) to amplify and sequence the V4–V5 region of the 16S ribosomal DNA analysis. The Meta-Stat computer program was used to assess the differences in the two communities. The sequences produced from all 12 samples were categorized into 1533 unique phylotypes, including 30 phyla, 81 classes, 270 families, and 414 genera. The top five dominant communities in the culture pond were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, and Acidobacteria, while Proteobacteria, Planctomycetes, Bacteroidetes, Actinobacteria, and Cyanobacteria were the dominant communities in the control pond. Higher abundance was observed in the culture pond at the phylum, class, and genus levels, and the same result was also observed in the rarefaction curves. Elusimicrobia, Fibrobacteres, Fusobacteria, Tenericutes, MVP-21, SM2F11, and WCHB1-60 were present, whereas Deferribacteres and Lentisphaerae, as well as the candidate divisions BRC1, OD1, and OP11, disappeared from the culture pond. Moreover, abundant phylotypes (Aeromonadaceae, Pseudomonadaceae, Enterobacteriaceae, Bradyrhizobiaceae, Clostridiaceae, and Xanthomonadaceae) were present in the culture pond, but only rarely present in the control pond. These results suggest that mariculture contributed to the change in bacterial communities in the culture pond compared with the non-culture pond. Proteobacteria was the most dominant community in both ponds, but the second most dominant community was Planctomycetes in the control pond and Chloroflexi in the culture pond. Seven new phyla were observed, but five phyla disappeared in the culture pond. The disease- or metabolism-related members of the bacterial communities, namely, Aeromonadaceae, Pseudomonadaceae, Enterobacteriaceae, and Xanthomonadaceae, were abundant phylotypes in the culture pond. Our results contribute to an improved understanding of the establishment and maintenance of the bacterial community structure in a complex aquaculture ecosystem and may have practical applications in terms of improving seawater quality and early disease warning in this popular mariculture model in China.

Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing.

Vinyl chloride (VC), a known human carcinogen, is a common and persistent groundwater pollutant at many chlorinated solvent contaminated sites. The remediation of such sites is challenging because of the lack of knowledge on the microorganisms responsible for in situ VC degradation. To address this, the microorganisms involved in carbon assimilation from VC were investigated in a culture enriched from contaminated site groundwater using stable isotope probing (SIP) and high-throughput sequencing. The mixed culture was added to aerobic media, and these were amended with labeled ((13)C-VC) or unlabeled VC ((12)C-VC). The cultures were sacrificed on days 15, 32, and 45 for DNA extraction. DNA extracts and SIP ultracentrifugation fractions were subject to sequencing as well as quantitative PCR (qPCR) for a functional gene linked to VC-assimilation (etnE). The gene etnE encodes for epoxyalkane coenzyme M transferase, a critical enzyme in the pathway for VC degradation. The relative abundance of phylotypes was compared across ultracentrifugation fractions obtained from the (13)C-VC- and (12)C-VC-amended cultures. Four phylotypes were more abundant in the heavy fractions (those of greater buoyant density) from the (13)C-VC-amended cultures compared to those from the (12)C-VC-amended cultures, including Nocardioides, Brevundimonas, Tissierella, and Rhodoferax. Therefore, both a previously identified VC-assimilating genus (Nocardioides) and novel microorganisms were responsible for carbon uptake. Enrichment of etnE with time was observed in the heavy fractions, and etnE sequences illustrated that VC-assimilators harbor similar Nocardioides-like etnE. This research provides novel data on the microorganisms able to assimilate carbon from VC.

Thermophilic prokaryotic communities inhabiting the biofilm and well water of a thermal karst system located in Budapest (Hungary).

In this study, scanning electron microscopy (SEM) and 16S rRNA gene-based phylogenetic approach were applied to reveal the morphological structure and genetic diversity of thermophilic prokaryotic communities of a thermal karst well located in Budapest (Hungary). Bacterial and archaeal diversity of the well water (73.7°C) and the biofilm developed on the inner surface of an outflow pipeline of the well were studied by molecular cloning method. According to the SEM images calcium carbonate minerals serve as a surface for colonization of bacterial aggregates. The vast majority of the bacterial and archaeal clones showed the highest sequence similarities to chemolithoautotrophic species. The bacterial clone libraries were dominated by sulfur oxidizer Thiobacillus (Betaproteobacteria) in the water and Sulfurihydrogenibium (Aquificae) in the biofilm. A relatively high proportion of molecular clones represented genera Thermus and Bellilinea in the biofilm library. The most abundant phylotypes both in water and biofilm archaeal clone libraries were closely related to thermophilic ammonia oxidizer Nitrosocaldus and Nitrososphaera but phylotypes belonging to methanogens were also detected. The results show that in addition to the bacterial sulfur and hydrogen oxidation, mainly archaeal ammonia oxidation may play a decisive role in the studied thermal karst system.

MOLECULAR DETECTION OF ANTIBIOTIC-RESISTANCE DETERMINANTS IN ESCHERICHIA COLI ISOLATED FROM THE ENDANGERED AUSTRALIAN SEA LION (NEOPHOCA CINEREA).

Greater interaction between humans and wildlife populations poses significant risks of anthropogenic impact to natural ecosystems, especially in the marine environment. Understanding the spread of microorganisms at the marine interface is therefore important if we are to mitigate adverse effects on marine wildlife. We investigated the establishment of Escherichia coli in the endangered Australian sea lion (Neophoca cinerea) by comparing fecal isolation from wild and captive sea lion populations. Fecal samples were collected from wild colonies March 2009-September 2010 and from captive individuals March 2011-May 2013. Using molecular screening, we assigned a phylotype to E. coli isolates and determined the presence of integrons, mobile genetic elements that capture gene cassettes conferring resistance to antimicrobial agents common in fecal coliforms. Group B2 was the most abundant phylotype in all E. coli isolates (n = 37), with groups A, B1, and D also identified. Integrons were not observed in E. coli (n = 21) isolated from wild sea lions, but were identified in E. coli from captive animals (n = 16), from which class I integrases were detected in eight isolates. Sequencing of gene cassette arrays identified genes conferring resistance to streptomycin-spectinomycin (aadA1) and trimethoprim (dfrA17, dfrB4). Class II integrases were not detected in the E. coli isolates. The frequent detection in captive sea lions of E. coli with resistance genes commonly identified in human clinical cases suggests that conditions experienced in captivity may contribute to establishment. Identification of antibiotic resistance in the microbiota of Australian sea lions provides crucial information for disease management. Our data will inform conservation management strategies and provide a mechanism to monitor microorganism dissemination to sensitive pinniped populations.

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts.

Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.

Characterization of mucosa-associated bacterial communities in abomasal ulcers by pyrosequencing

Abomasal ulcers are important pathological alterations of the gastrointestinal tract in cattle and are exceptionally hard to diagnose in vivo. The microbiome of the abomasum in cattle with or without ulcers has hardly been studied to date, and if so, the studies used culture-dependent methods. In the present study, the bacterial communities associated with abomasal ulcers of slaughter cows, bulls, and calves in Austria were described using 16S rRNA gene pyrosequencing. Sequences were clustered into 10,459 operational taxonomic units (OTUs), affiliating to 28 phyla with Proteobacteria, Firmicutes, Bacteroidetes and Tenericutes dominating (96.4% of all reads). The most abundant genera belonged to Helicobacter, Acetobacter, Lactobacillus, and novel Mycoplasma-like phylotypes. Significant differences between the microbial communities of healthy and ulcerated calves compared to cows and bulls could be observed. However, only few statistically significant differences in the abundances of certain OTUs between healthy and ulcerated abomasal mucosa were found. Additionally, near full-length 16S rRNA gene sequences of the most abundant phylotypes were obtained by cloning and Sanger sequencing (n=88). In conclusion, our results allow the first deep insights into the composition of abomasal mucosal bacterial communities in cattle and describe a hitherto unknown high diversity and species richness of abomasal bacteria in cattle. Our results suggest that bacteria may have only limited involvement in the etiology of abomasal ulcers. However, future research will be needed to verify the contribution of bacteria to abomasal ulcer formation as presence or absence of bacteria does not necessarily correlate with etiology of disease.

Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site.

This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

Impact of a probiotic, inulin, or their combination on the piglets' microbiota at different intestinal locations.

Natural feed additives are used to maintain health and to promote performance of pigs without antibiotics. Effects of a probiotic, inulin, and their combination (synbiotic), on the microbial diversity and composition at different intestinal locations were analysed using denaturing gradient gel electrophoresis (DGGE), real-time PCR, and 16S rRNA gene pyrosequencing. Bacterial diversity assessed by DGGE and/or pyrosequencing was increased by inulin in all three gut locations and by the synbiotic in the caecum and colon. In contrast, the probiotic did only affect the microbiota diversity in the ileum. Shifts in the DGGE microbiota profiles of the caecum and colon were detected for the pro- and synbiotic fed animals, whereas inulin profiles were more similar to the ones of the control. 16S rRNA gene pyrosequencing revealed that all three additives could reduce Escherichia species in each gut location, indicating a potential beneficial effect on the gut microbiota. An increase of relative abundance of Clostridiaceae in the large intestine was found in the inulin group and of Enterococcaceae in the ileum of probiotic fed pigs. Furthermore, real-time PCR results showed that the probiotic and synbiotic increased bifidobacterial numbers in the ileum, which was supported by sequencing results. The probiotic and inulin, to different extents, changed the diversity, relative abundance of phylotypes, and community profiles of the porcine microbiota. However, alterations of the bacterial community were not uniformly between gut locations, demonstrating that functionality of feed additives is site specific. Therefore, gut sampling from various locations is crucial when investigations aim to identify the composition of a healthy gut microbiota after its manipulation through feed additives.

Bacterial community structure in maize residue amended soil with contrasting management practices

Agricultural practices affect the bacterial community structure in soil. It was hypothesized that agricultural practices would also affect the bacteria involved in the degradation of crop residue. Soil was sampled from four different agricultural practices, i.e. conventional agriculture on the flat or on beds, or conservation agriculture on the flat or on beds. Cultivating crops on the flat is done traditionally, but cultivating crops on beds was introduced so as to avoid water logging during the rainy season and its potential negative effect on yields. Soil from these four treatments was amended in the laboratory with maize residue (Zea mays L.) or its neutral detergent fibre (NDF) fraction, mostly consisting of (hemi) cellulose, and incubated aerobically for 14 days. Maize residue was applied to soil as it is left in the field in conservation agriculture and NDF was added to study which bacteria were favoured by application of (hemi) cellulose. Soil was incubated aerobically while the carbon mineralization and the bacterial population were monitored. On the one hand, the relative abundance of phylotypes belonging to bacterial groups that preferred low nutrient environments was higher in soil with conservation agriculture (e.g. Acidobacteria 17.6%, Planctomycetes 1.7% and Verrucomicrobia 1.5%) compared to conventional practices (Acidobacteria 11.8%, Planctomycetes 0.9% and Verrucomicrobia 0.4%). On the other hand, the relative abundance of phylotypes belonging to bacterial groups that preferred nutrient rich environments, such as Actinobacteria, showed an opposite trend. It was 11.9% in conservation agriculture and 16.2% in conventional practices. The relative abundance of Arthrobacter (Actinobacteria) and Bacillales more than doubled when maize residue was applied to soil compared to the unamended soil and that of Actinomycetales when maize or NDF was applied. Application of organic material reduced the relative abundance of a wide range of bacterial groups, e.g. Acidobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia. It was found that application of organic material favoured the same bacterial groups that were more abundant in the soil cultivated conventionally while it reduced those that were favoured in conservation agriculture.

Sources of iron and phosphate affect the distribution of diazotrophs in the North Atlantic

Biological nitrogen fixation (BNF) supplies nutrient-depleted oceanic surface waters with new biologically available fixed nitrogen. Diazotrophs are the only organisms that can fix dinitrogen, but the factors controlling their distribution patterns in the ocean are not well understood. In this study, the relative abundances of eight diazotrophic phylotypes in the subtropical North Atlantic Ocean were determined by quantitative PCR (qPCR) of the nifH gene using TaqMan probes. A total of 152 samples were collected at 27 stations during two GEOTRACES cruises; Lisbon, Portugal to Mindelo, Cape Verde Islands (USGT10) and Woods Hole, MA, USA via the Bermuda Time Series (BATS) to Praia, Cape Verde Islands (USGT11). Seven of the eight diazotrophic phylotypes tested were detected. These included free-living and symbiotic cyanobacteria (unicellular groups (UCYN) A, B and C, Trichodesmium, the diatom-associated cyanobacteria Rhizoselinia–Richelia and Hemiaulus–Richelia) and a γ-proteobacterium (Gamma A, AY896371). The nifH gene abundances were analyzed in the context of a large set of hydrographic parameters, macronutrient and trace metal concentrations measured in parallel with DNA samples using the PRIMER-E software. The environmental variables that most influenced the abundances and distribution of the diazotrophic phylotypes were determined. We observed a geographic segregation of diazotrophic phylotypes between east and west, with UCYN A, UCYN B and UCYN C and the Rhizosolenia–Richelia symbiont associated with the eastern North Atlantic (east of 40°W), and Trichodesmium and Gamma A detected across the basin. Hemiaulus–Richelia symbionts were primarily found in temperate waters near the North American coast. The highest diazotrophic phylotype abundance and diversity were associated with temperatures greater than 22°C in the surface mixed layer, a high supply of iron from North African aeolian mineral dust deposition and from remineralized nutrients upwelled at the edge of the oxygen minimum zone off the northwestern coast of Africa.