The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetateoxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

Campylobacter jejuni colonization of chickens is presumably dependent upon multiple surface-exposed proteins termed adhesins. Putative C. jejuni adhesins include CadF, CapA, JlpA, major outer membrane protein, PEB1, Cj1279c, and Cj1349c. We examined the genetic relatedness of 97 C. jejuni isolates recovered from human, poultry, bovine, porcine, ovine, and canine sources by multilocus sequence typing (MLST) and examined their profile of putative adhesin-encoding genes by dot blot hybridization. To assess the individual contribution of each protein in bacterium-host cell adherence, the C. jejuni genes encoding the putative adhesins were disrupted by insertional mutagenesis. The phenotype of each mutant was judged by performing in vitro cell adherence assays with chicken LMH hepatocellular carcinoma epithelial cells and in vivo colonization assays with broiler chicks. MLST analysis indicated that the C. jejuni isolates utilized in this study were genetically diverse. Dot blot hybridization revealed that the C. jejuni genes encoding the putative adhesins, with the exception of capA, were conserved among the isolates. The C. jejuni CadF, CapA, Cj1279c, and Cj1349c proteins were found to play a significant role in the bacterium's in vitro adherence to chicken epithelial cells, while CadF, PEB1, and Cj1279c were determined to play a significant role in the bacterium's in vivo colonization of broiler chicks. Collectively, the data indicate that Cj1279c is a novel adhesin. Because Cj1279c harbors fibronectin type III domains, we designated the protein FlpA, for fibronectin-like protein A.

The theoretical description of the forces that shape ecological communities focuses around two classes of models. In niche theory, deterministic interactions between species, individuals, and the environment are considered the dominant factor, whereas in neutral theory, stochastic forces, such as demographic noise, speciation, and immigration, are dominant. Species abundance distributions predicted by the two classes of theory are difficult to distinguish empirically, making it problematic to deduce ecological dynamics from typical measures of diversity and community structure. Here, we show that the fusion of species abundance data with genomederived measures of evolutionary distance can provide a clear indication of ecological dynamics, capable of quantifying the relative roles played by niche and neutral forces. We apply this technique to six gastrointestinal microbiomes drawn from three different domesticated vertebrates, using high-resolution surveys of microbial species abundance obtained from carefully curated deep 16S rRNA hypervariable tag sequencing data. Although the species abundance patterns are seemingly well fit by the neutral theory of metacommunity assembly, we show that this theory cannot account for the evolutionary patterns in the genomic data; moreover, our analyses strongly suggest that these microbiomes have, in fact, been assembled through processes that involve a significant nonneutral (niche) contribution. Our results demonstrate that high-resolution genomics can remove the ambiguities of process inference inherent in classic ecological measures and permits quantification of the forces shaping complex microbial communities.metagenomics | microbial ecology E cological species distributions are determined by the interplay between environmental factors and evolutionary processes. In classic ecological theory, niches characterized by nutrients and other environmental factors, for example, determine species abundance distributions and populations primarily through deterministic partitioning of resources among species (1). Species populations are limited by niche-carrying capacity rather than by interspecies competition, thus tending to promote coexistence (2). In niche theory, diversity is determined primarily by the number of available niches, raising the issue of how to account quantitatively for the apparent observed diversity (3-6) from well-documented instances of niche differences (7).An alternative perspective is the class of neutral theories in which species are functionally equivalent and stochastic factors, such as immigration, birth/death processes, and speciation, are the primary drivers of ecological diversity and community structure (8-13). This class of models has been reported to be capable of accurate predictions for the species abundance distributions in riverine fish populations (14) or microbial populations (15), for example, in addition to the early successes in forest ecosystems, a planktonic copepod community, and a bat community on Barro Colorado Island (BCI) (10). Ho...

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The methanogenic community in hydrothermally active sediments of Guaymas Basin (Gulf of California, Mexico) was analyzed by PCR amplification, cloning, and sequencing of methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Members of the Methanomicrobiales and Methanosarcinales dominated the mcrA and 16S rRNA clone libraries from the upper 15 cm of the sediments. Within the H 2 /CO 2 -and formate-utilizing family Methanomicrobiales, two mcrA and 16S rRNA lineages were closely affiliated with cultured species of the genera Methanoculleus and Methanocorpusculum. The most frequently recovered mcrA PCR amplicons within the Methanomicrobiales did not branch with any cultured genera. Within the nutritionally versatile family Methanosarcinales, one 16S rRNA amplicon and most of the mcrA PCR amplicons were affiliated with the obligately acetate utilizing species Methanosaeta concilii. The mcrA clone libraries also included phylotypes related to the methyl-disproportionating genus Methanococcoides. However, two mcrA and two 16S rRNA lineages within the Methanosarcinales were unrelated to any cultured genus. Overall, the clone libraries indicate a diversified methanogen community that uses H 2 /CO 2 , formate, acetate, and methylated substrates. Phylogenetic affiliations of mcrA and 16S rRNA clones with thermophilic and nonthermophilic cultured isolates indicate a mixed mesophilic and thermophilic methanogen community in the surficial Guaymas sediments.The hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) have an active methane cycle, with two major sources and several potential sinks of methane. Diffuse venting through the Guaymas sediments at temperatures up to 200°C leads to pyrolysis of organic material in the organic-rich sediments (maximal total organic carbon concentration, 3 to 12% [wt/wt] near the surface [25]). Pyrolysis products include significant amounts of aliphatic and aromatic petroleum hydrocarbons, short-chain fatty acids, ammonia, and methane (2, 30, 57). The methane content in the Guaymas hydrothermal fluids ranges from 12 to 16 mM (270 to 370 ml kg Ϫ1 at standard temperature and pressure), which is approximately 2 orders of magnitude higher than those of most bare lava vent sites (57). The carbon isotopic composition (␦ 13 C) of Guaymas methane ranges from Ϫ51 to Ϫ41‰, suggesting a predominantly thermocatalytic origin from sedimentary organic material (37, 57).Diverse communities of methanogenic archaea produce methane in the Guaymas sediments. Several hyperthermophilic methanogens, including members of the genus Methanococcus (recently renamed Methanocaldococcus) and the most thermophilic methanogen identified to date, Methanopyrus kandleri, have been isolated from the Guaymas sediments (19,21,22,23,24). Based on initial 16S rRNA gene surveys, the methanogen communities of Guaymas also include relatives of mesophilic species and genera within the families Methanomicrobiales and Methanosarcinales (50). In some localities near the sediment surface, abundant methanotrop...