Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral sulfur cycle by metabolizing dimethylsulfoniopropionate (DMSP) into dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) draft genomes of strains of the recently added species Endozoicomonas acroporae (Acr-14 T , Acr-1, and Acr-5) isolated from the coral Acropora sp. and performed a comparative genomic analysis on the genus Endozoicomonas. We identified DMSP CoA-transferase/lyase-a dddD gene homolog in all sequenced genomes of E. acroporae strains-and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as a carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

Halovirus PH1 infects Haloarcula hispanica and was isolated from an Australian salt lake. The burst size in single-step growth conditions was 50–100 PFU/cell, but cell density did not decrease until well after the rise (4–6 hr p.i.), indicating that the virus could exit without cell lysis. Virions were round, 51 nm in diameter, displayed a layered capsid structure, and were sensitive to chloroform and lowered salt concentration. The genome is linear dsDNA, 28,064 bp in length, with 337 bp terminal repeats and terminal proteins, and could transfect haloarchaeal species belonging to five different genera. The genome is predicted to carry 49 ORFs, including those for structural proteins, several of which were identified by mass spectroscopy. The close similarity of PH1 to SH1 (74% nucleotide identity) allowed a detailed description and analysis of the differences (divergent regions) between the two genomes, including the detection of repeat-mediated deletions. The relationship of SH1-like and pleolipoviruses to previously described genomic loci of virus and plasmid-related elements (ViPREs) of haloarchaea revealed an extensive level of recombination between the known haloviruses. PH1 is a member of the same virus group as SH1 and HHIV-2, and we propose the name halosphaerovirus to accommodate these viruses.

Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73 ± 0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24±0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.

Species of bacteria associated with Stylophora pistillata were determined by analyses of 16S ribosomal genes. Coral samples were taken from two distinct sites at Kenting, in the far south of Taiwan; three coral colonies at each site were tagged and sampled in the winter and summer of 2007. Six hundred 16S rRNA gene clones were selected and sequenced for diversity analysis and community comparison. LIBSHUFF and nonparametric multiple dimensional scaling analyses showed variations in the composition of the coral-associated bacteria in the different samples, suggesting that seasonal and geographic factors and variations in individual coral colonies were all vital drivers of the structure of the S. pistillata-associated bacterial community. To examine the association between species specificity and environmental impacts on the structure of the coral-associated bacterial community, we conducted an integrated, comparative analysis of 44 coral-associated bacterial data sets, including the present study's data. The clustering analysis suggests that the influence of spatial and temporal factors on the coral-associated bacteria population structure is considerable; nonetheless, the effect of species specificity is still detectable in some coral species, especially those from the Caribbean Sea.

Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.