Characterisation of the Prokaryotic community of Lake Suigetsu, Japan: towards a novel palaeoenvironment research biomarker

Abstract

Sediment cores from Lake Suigetsu, Japan are recognised as a key record of past climate reconstruction because of the finely laminated sediments that provide precise event stratigraphy. Here, we study the relationship between the microbial communities in the lake sediments of Lake Suigetsu during validated episodes of environmental change. We use fossil DNA from the lake sediment and utilising the PCR-DGGE technique, we detected the presence of several taxa. Among the investigated sediment cores, the Acidobacteria community was found to be the most abundant while the Actinobacteria community was the least. The results showed that the overall bacterial community structure and their diversity were significantly affected by sediment depths, rather than the availability of nutrient (i.e. TOC and TN). The first event was the introduction of saline water in Lake Suigetsu. Historical records have described this event occurring during 1664 AD, which equates to the sediment depth of approximately 81.64 cm. A metagenomics study based on selected sediment depths has exhibited a shift in the bacterial taxa, consistent with the transition of lake salinity from freshwater to brackish. Bacillaceae and Clostridiaceae were found to be more predominant in the brackish sediments relative to the freshwater sediments. Evidence of the seawater incursion was found in the sediment depths between 82.16 and 83.16 cm. The second event was a climate event dated back to the Late Quaternary period. The results presented here show that bacterial diversity and species richness become increased when climate changed from a cold to warmer conditions. The metagenomics analysis on the sediment deposits has demonstrated distinctive differentiations in bacterial taxa during the climate transition from the colder to warmer episodes. This observation could be related to the rapid adaptation/tolerance of bacteria to environmental changes, or simply the effect of depth. Although the temperature-dependent δ15N isotope can be strongly correlated to the bacterial communities, the weak selectivity of the δ15N isotope could result in false correlation between the δ15N isotope and the diversity of the bacterial communities. The application of molecular and culture-dependent techniques was used to characterise bacterial diversity in the sedimentary records of Lake Suigetsu. The culture-based techniques showed a better representation of high GC Actinobacteria while molecular techniques revealed a better profile of Gram negative bacteria. Furthermore, based on a polyphasic approach, several putatively new species have been identified, notably Actinobacteria strains that belong to the genera Dermacoccus, Dietzia, Leifsonia and Rhodococcus. Among the tested strains, a novel Rhodococcus isolate that was recovered from the freshwater sediment, merits recognition of new species status and the name Rhodococcus meromictica sp. nov is proposed