Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding ‘higher’ Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H_2 metabolism, CO_2-reductive acetogenesis and N_2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-μl environment can be

A Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersal

This report talks about Bacterial Metapopulation Adapts Locally to Phage Predation Despite Global Dispersa

Diversity and ecology of freshwater actinobacteria

Actinobacteria are highly abundant in freshwater bacterioplankton. However, little is known about their diversity, distribution, physiology and ecological role in the aquatic environment. In this thesis the rRNA approach was applied to elucidate the diversity and distribution of freshwater Actinobacteria (limnic Actinobacteria = LAB). The selected cloning strategy and a specifically designed screening method yielded many nearly complete 16S rRNA sequences originating from diverse freshwater habitats. Thereby, the available sequence dataset and the awareness of diversity of LAB was comprehensively expanded.Comparative Sequence analysis revealed that most sequence motifs along with published sequences from mainly freshwater habitats formed four monophyletic clades. The newly defined clusters acI to acIV were distinct from those from marine habitats and soils. Based on phylogenetic reconstructions specific probes for fluorescence-in situ-hybridization (FISH) were designed to analyze the population structure of LAB. For five probes stringent hybridization conditions were determined by custom-developed testing strategies. The application of these probes demonstrated the abundance and importance of the actinobacterial acI-cluster in freshwater bacterioplankton. A subset of three probes targeting subgroups of the acI-cluster revealed differences in the community composition between different lakes. Clones of the acII-cluster appeared equally abundant in 16S rRNA gene libraries, but the respective organisms were of minor numerical importance in the investigated habitats.In a field study ten high mountain lakes in the Tyrolean Alps (Austria) were sampled. These lakes differed in e.g. their altitude and the water visibility leading to distinct exposures of aquatic organisms to UV-B radiation. The UV-B radiation damages DNA mainly by dimerisation of adjacent thymin bases. The genomic DNA of Actinobacteria contains a high molar G C content and thus a higher number of CC-dimers than TT-dimers. CC-dimers are thermodynamically more stable. Thus, bacteria with genomes rich in G C likely are more resistant to UV-B radiation. Therefore the hypothesis was tested, if there is a link between the relative abundance of LAB and the exposure to UV-B in surface layers of high mountain lakes. A positive correlation (r2=0,73) between the abundances of Actinobacteria and UV-B was shown for high mountain lakes above the timberline, whereas no correlation was found for two lakes at lower altitudes. Previous studies have speculated that LAB are relatively inactive organisms surviving mainly due to their resistance to grazing by protists. To test this hypothesis DNA-synthesizing populations in high mountain lakes were identified. The results indicate that the proportion of active cells of all Actinobacteria was similar to the average proportion of active bacterial cells of total bacteria. A clear preference of LAB for glucose-uptake was found in lake Fuchskuhle as demonstrated by combined micro-autoradiography and FISH (MAR-FISH). In cultivation attempts in the laboratory, growth of representatives of the environmentally important acI cluster was successfully stimulated. Future studies will focus on isolation of these bacteria into pure culture. This thesis gives clear evidence that Actinobacteria of the acI cluster are an abundant and metabolically active group of freshwater bacterioplankton. Hence, they constitute an important autochthonous part of such microbial communities

Bloom of Filamentous Bacteria in a Mesotrophic Lake: Identity and Potential Controlling Mechanism

Ephemeral blooms of filamentous bacteria are a common phenomenon in the water column of oligo- to mesotrophic lakes. It is assumed that the appearance of such morphotypes is favored by selective predation of bacterivorous protists and that filter-feeding zooplankton plays a major role in suppressing these bacteria. The phylogenetic affiliation of the important bloom-forming filamentous bacteria in freshwaters is presently unknown. Here we report the identification of dominant members of a filamentous bacterial assemblage during a bloom of such morphotypes in a mesotrophic lake. By molecular cloning and fluorescence in situ hybridization with specific oligonucleotide probes, up to 98% of filamentous cells in lake water could be assigned to a clade of almost identical (99% similarity) 16S rRNA gene sequence types, the cosmopolitan freshwater LD2 cluster. For a period of less than 1 week, members of the LD2 clade constituted >40% of the total bacterial biomass, potentially favored by high grazing of planktivorous protists. This is probably the most pronounced case of dominance by a single bacterioplankton species ever observed in natural freshwaters. In enclosures artificially stocked with the metazoan filter feeder Daphnia, bacteria related to the LD2 clade formed a significantly larger fraction of filaments than in enclosures where Daphnia had been removed. However, in the presence of higher numbers of Daphnia individuals, the LD2 bacteria, like other filaments, were eventually eliminated both in enclosures and in the lake. This points at the potential importance of filter-feeding zooplankton in controlling the occurrence and species composition of filamentous bacterial morphotypes in freshwater plankton

Abundances, Identity, and Growth State of Actinobacteria in Mountain Lakes of Different UV Transparency

The occurrence, identity, and activity of microbes from the class Actinobacteria was studied in the surface waters of 10 oligo- to mesotrophic mountain lakes located between 913 m and 2,799 m above sea level. Oligonucleotide probes were designed to distinguish between individual lineages within this group by means of fluorescence in situ hybridization (FISH). Bacteria of a single phylogenetic lineage (acI) represented >90% of all Actinobacteria in the studied lakes, and they constituted up to 70% of the total bacterial abundances. In the subset of eight lakes situated above the treeline, the community contribution of bacteria from the acI lineage was significantly correlated with the ambient levels of solar UV radiation (UV transparency, r(2) = 0.72; P < 0.01). Three distinct genotypic subpopulations were distinguished within acI that constituted varying fractions of all Actinobacteria in the different lakes. The abundance of growing actinobacterial cells was estimated by FISH and immunocytochemical detection of bromodeoxyuridine (BrdU) incorporation into de novo-synthesized DNA. The percentages of Actinobacteria with visible DNA synthesis approximately corresponded to the average percentages of BrdU-positive cells in the total assemblages. Actinobacteria from different subclades of the acI lineage, therefore, constituted an important autochthonous element of the aquatic microbial communities in many of the studied lakes, potentially also due to their higher UV resistance