Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal vents

Our understanding of the role of viruses in surface communities is beginning to unfold. In comparison, the role of viruses in deep and shallow hydrothermal vent communities is still largely unknown. Yoshida-Takashima and colleagues analysed the viral communities of deep sea and shallow hydrothermal vents in attached and planktonic microbial habitats. The two sites chosen for this investigation were Hatoma Knoll, deep sea vent, located at the southern Okinawa trough, Japan at 1,457m depth. The second sight was located off Taketomi island, Okinawa,  at depths between 13 and 20m. Samples from the deep vent were collected using an ROV, samples from the shallow water vent were collected using divers. Water was collected from just above macrofaunal communities, from within the hydrothermal vent fluid. Samples were also collected from the macrofauna of the vent communities. This included collection of the ventral setae of Galatheid crabs an and the nests of polychaete worms. From the shallow vent site samples form microbial mats and surrounding water were collected. Samples for prokaryote and virus-like-particle (VLP) count were stored in formaldehyde and stored at -80ºC. Prokaryotes and VLP abundance was determined with DAPI and SYBR gold stained sample using fluorescence microscopy. Genetic diversity was ascertained by quantative PCR for small-subunit (SSU) rRNA genes. Each 16s rRNA gene phylotypes was inserted into the reference tree using parsimony insertion algorithm in ARB software an phylogenetically classified into taxonomic units using Hugenholtz small sub-unit rRNA sequence database and phylogenetic classification. Similarities/differences among 16s rRNA gene communities used Jackknife environment cluster analysis in the unifract program. Prokaryote abundance followed the pattern; surrounding water, vent habitat, macro-fauna associated habitats with the highest abundance on the setae of galatheid crabs. The attached microbial community showed higher abundance than the planktonic community. The macrofaunal-associated communities showed the greatest variation in the data, showing the highest and lowest abundance between all habitats. The shallow vents community appeared to show the opposite trend with planktonic communities showing higher abundances than attached communities, but no variation is stated so it suggests that only one sample may have been available.   A considerable proportion of the paper by Yoshida-Takashima and colleagues assess the prokaryotic community structure and abundance. No attempt to assess the phylogenetic relationships of the viral community was made.

The virus-prokaryote ratio (VPR) was highly variable in both shallow and deep sea planktonic communities. The VLP abundance was plotted against the prokaryote abundance, but showed no correlation. The VLP abundance was highly variable in the attached communities for deep sea vents.  For the shallow vent community data for VLP was only available for the microbial mats at the main site. The authors suggest that the attached microbial community of both deep sea and shallow water hydrothermal vents was significantly positively correlated with the whole prokaryotic cell abundance. This is the case for deep sea microbial mats, but close inspection of the graph only shows one data point for the shallow vent community, so I think this claim should be disregarded. The main point of this paper is that viral abundance in attached microbial communities increases with prokaryote abundance. Given the amount of time and money that must have gone into this project this seems to be quite a disappointing result. Towards the end of the paper the authors suggest that the use of formaldehyde may have caused anomalies in the viral counts, because it has been shown to cause viral degradation. Overall this paper gave a lot of information on the prokaryotic community, but not very much on the viruses.         

Yoshida-Takashima, Takuro Nunoura, Hironori Yukari, Kazuhiro Inoue, Takuroh Noguchi, Kazama Masahiro, Tomohiro Toki,Toshiro Yamanaka, Akashi Hiroyuki Yuichiro, Ueno Yamamoto, Takai Yamamoto.,(2012) Appl. Environ. Microbiol. 78(5):1311. DOI: 10.1128/AEM.06491-11.

http://aem.asm.org/content/78/5/1311.full.pdf