Effects of Habitat Partitioning on the Distribution of Bacterioplankton in Deep Lakes

Abstract

In deep lakes, many investigations highlighted the existence of exclusive groups of bacteria adapted to deep oxygenated and hypoxic and anoxic hypolimnia. Nevertheless, the extent of bacterial strain diversity has been much less scrutinized. This aspect is essential for an unbiased estimation of genetic variation, biodiversity, and population structure, which are essential for studying important research questions such as biogeographical patterns, temporal and spatial variability and the environmental factors affecting this variability. This study investigated the bacterioplankton community in the epilimnetic layers and in the oxygenated and hypoxic/anoxic hypolimnia of five large and deep lakes located at the southern border of the Alps using high throughput sequencing (HTS) analyses (16S rDNA) and identification of amplicon sequence variants (ASVs) resolving reads differing by as little as one nucleotide. The study sites, which included two oligomictic (Garda and Como) and three meromictic lakes (Iseo, Lugano, and Idro) with maximum depths spanning from 124 to 410 m, were chosen among large lakes to represent an oxic-hypoxic gradient. The analyses showed the existence of several unique ASVs in the three layers of the five lakes. In the case of cyanobacteria, this confirmed previous analyses made at the level of strains or based on oligotyping methods. As expected, the communities in the hypoxic/anoxic monimolimnia showed a strong differentiation from the oxygenated layer, with the exclusive presence in single lakes of several unique ASVs. In the meromictic lakes, results supported the hypothesis that the formation of isolated monimolimnia sustained the development of highly diversified bacterial communities through ecological selection, leading to the establishment of distinctive biodiversity zones. The genera identified in these layers are well-known to activate a wide range of redox reactions at low O2 conditions. As inferred from 16S rDNA data, the highly diversified and coupled processes sustained by the monimolimnetic microbiota are essential ecosystem services that enhance mineralization of organic matter and formation of reduced compounds, and also abatement of undesirable greenhouse gasses.

Permanent Thermal and Chemical Stratification in a Restored Urban Meromictic Lake

“…A reduction in the amount of hydrogen sulphide, which is released into the atmosphere as a result of gas convection and erosion of monimolimnion, has also been observed [2,3]. In the lake under study, distinct changes in the structure of bacterial plankton at a depth of 15 m (e.g., a high proportion of large, rod-shaped sulphur-reducing bacteria [8] that are characteristic of meromictic lakes or lakes with an anoxic hypolimnion [59] were observed) indicate that environmental and trophic conditions remained stable between the depth of 15 m and the lake bottom. The analysed lake was abundant in organic matter.…”

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

“…The results obtained from the applications of HTS to freshwater samples are impressive and are unveiling a degree of diversity in biological communities previously unimaginable, including a significant presence of the new group of non-photosynthetic cyanobacteria (Shih et al, 2013(Shih et al, , 2017Salmaso et al, 2018;Monchamp et al, 2019;Salmaso, 2019). Nonetheless, the application of these techniques is not free from difficulties, due to (among the others) the semiquantitative nature of data, the short DNA reads obtained by the most common HTS techniques, the variability in the copy number per cell of the most common taxonomic markers used (i.e.…”

Unraveling the Diversity of Eukaryotic Microplankton in a Large and Deep Perialpine Lake Using a High Throughput Sequencing Approach

“…For the reasons above, the interpretation of diversity based on ASVs should take into account its multifaceted nature. ASVs do not correspond to species or even lower taxonomic levels, rather they represent different oligotypes of these same or different taxonomic levels, and even individuals (Eren et al, 2013;Salmaso, 2019). If focused on the evaluation of classical diversity estimations, downstream analyses should therefore consider unique taxa agglomerated at different taxonomic ranks, e.g., Supplementary Tables 1, 2, which however do not include all the unclassified taxa at the genus and/or family levels.…”