Salt: A microbial preference?

A review of Hollister, B. E. et al (2010) Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments, The ISME Journal. 4, 829-838

Across the globe, microbes can be found adapting and living in numerous extreme environments. One example is hypersaline environments, such as salt lakes, hypersaline springs and solar salterns, which sustain diverse microbial communities. Lozupone and Knight 2007, established that levels of salinity are a major factor in determining the composition of microbial communities. Moreover, recent global surveys have confirmed that sediment environments sustain more phylogenetically diverse bacterial communities than any other environment. Despite this, the majority of research published on microbial diversity in hypersaline ecosystems has been focused on aquatic environments only. This has allowed for a better understanding of the biology of extreme environments while also discovering novel organisms as well as enzymes with potential for various biotechnological applications, but has also pointed out the necessity for similar research to be done on sediment and soil communities.

The research was focused at La Sal del Ray, a naturally occurring salt lake in southern Texas, whose diversity and microbial communities have not been characterised. 8 samples were taken along a transect placed across the shoreline and lake sediment, The samples were chemically and physically analysed, recording properties such as pH, water content and salinity, and along with quantitative PCR, 16s rRNA tag-pyrosequencing and multivariate statistics, they were used to identify the microbial communities present and to establish the relationships they share with their environment.

The tests indicated that bacteria accounted for 97% of all the rRNA copies detected. Despite the limited abundance of Archaea, distribution patterns were found, as they were absent in the terrestrial sites and slowly increased in population (up to 8%) along the transect to the aquatic sites. Limited correlation between their abundance and sodium content was also found, suggesting a strong correlation between Archaeal abundance and water content. Significance tests confirmed correlation between community diversity and the sample water, pH and total inorganic carbon content and the Shannon diversity index value supported this showing diversity and community size decreasing as conditions became more water-logged and salt-rich. To establish the diversity and richness, 16s rRNA cloning and sequencing was conducted and found 16596 unique OTUs overall. Around 24 bacterial and 2 Archaeal phyla were detected, with Proteobacteria and Bacteroidetes being the most frequently encountered.

The authors concluded that the distribution of OTUs in the lake were either site-specific, occurring in only one of the sites, or cluster-specific, the clusters being terrestrial, intermediate or aquatic. They were also able to show which communities preferred higher or lower levels of salinity. For example, Acidobacteria and Rhodobacteraceae were detected in all the sites, however their abundance varied as Acidobacteria abundance declined as the conditions became more salt-rich and water-logged and instead, Rhodobacteraceae abundance increased. Similarly, many other site-specific or cluster-specific organisms were found, increasing our understanding of the salt lake microbial distribution and specifically what preferences they each have to salinity.

However, by assessing their results overall, it was concluded that although salinity has a major function in determining community composition at global scales, in regard to this study area and in salt-rich systems, they have little influence. Instead, the composition along the transect is based on microbial requirements for oxygen, carbon substrates that they metabolise and the range of pH they can tolerate. This is supported by the high correlation between microbial communities and water-logging, as although oxygen levels were not measured directly, water content is a good indicator of oxygen and thus supports the theory that microbes ultimately distribute to areas based on the oxygen availability.

The study has produced significant and detailed results. The researchers expanded their study by introducing variables such as different conditions for example, pH, organic carbon and calcium content and how microbial distribution correlates with them. This makes the study more representative by assessing many aspects of the ecosystem instead of just focusing on one, also making data more reliable and less bias. They have also taken into consideration possible errors when using PCR and pyrosequencing and have tried to reduce these as much as possible by using a combination of techniques which reduces individual errors and bias of each method and gives us a more detailed picture of the communities. The study also compared their results to previous studies focusing on hypersaline environments and found that the relative abundance of many of the dominant species they detected were very similar to the results of the other studies, further supporting the accuracy of the data and expanding the field of knowledge regarding global hypersaline microbial communities.

The authors established that around half of the estimated diversity of the communities were detected through sequencing and that some bacterial species found could not be identified. It would be interesting to find out a more accurate figure of the different species present by further PCR and sequencing, and through larger gene libraries, identify the unknown bacteria.

Other references:

Lozupone C.A, Knight R, (2007). Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104: 11436-11440