Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau

Abstract

Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated β-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated β-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of β-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in β-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.

Organic matter content and source is associated with the depth‐dependent distribution of prokaryotes in lake sediments

“…(2018). Members of the phylum Bacteroidota are generally present in the surface sediment layers in lakes and rivers (Newton et al., 2011; Zhu et al., 2023) because they are involved in the first step of OM degradation. The relative abundances of primary and secondary fermenters (i.e., Acetothermia) increased with sediment depth, consistent with the results from Vuillemin et al.…”

“…(2018). Spirochaeota are obligate fermenters using extracellular hydrolases and fermentation pathways to recycle biomass allowing them to thrive in anaerobic environments and thus resulting in their viability in lake sediments (Rissanen et al., 2019; Zhu et al., 2023). The observed variation in relative abundances of known denitrifiers (i.e., Alphaproteobacteria), sulfur oxidisers (i.e., Gammaproteobacteria), sulfate reducers (i.e., Desulfobacterota), methanogenesis or methane (CH 4 ) producers (i.e., Thermoplasmatota) with depth also are consistent with previous works (Dyksma et al., 2016; Liao et al., 2022; Vuillemin et al., 2018; Yang et al., 2017; Zhu et al., 2023).…”

“…The environmental selection of prokaryotes in surface sediments is strongly linked to the depletion of electron acceptors used for anaerobic microbial respiration (e.g., Parkes et al, 2005;Walsh et al, 2016). Indeed, as in marine sediments, the availability of electron acceptors decreased with increasing sediment depth (Nelson, 1997;Wurzbacher et al, 2017;Zhu et al, 2023), leading to depth-related stratification in the composition of the prokaryotic community in freshwater sediments.…”

“…Even though the vertical distribution of prokaryotes has been studied in freshwater sediments (i.e., Borrel et al., 2012; Kallmeyer et al., 2015; Liao et al., 2022; Thomas & Ariztegui, 2019; Villaescusa et al., 2011; Vuillemin et al.,2013, 2018; Wurzbacher et al., 2017), few studies have obtained adequate sampling resolutions and long‐sequence records to relate their community to geochemical features of the sediment. For instance, studies included a 30‐cm depth record from an oligo‐mesotrophic hardwater lake in northeast Germany (Wurzbacher et al., 2017), a 50‐cm sediment core from a eutrophic Lake Chaohu in central China (Li et al., 2019), a 26‐cm‐long sediment core record from a small boreal humic lake in southern Finland (Rissanen et al., 2019), and a 45‐cm sediment core from eastern Tibetan plateau's lakes (Zhu et al., 2023). Those records support previous evidence (Berner, 1980) that the composition of both bacterial and archaeal assemblages changes significantly with sediment depth/age.…”

“…The environmental selection of prokaryotes in surface sediments is strongly linked to the depletion of electron acceptors used for anaerobic microbial respiration (e.g., Parkes et al., 2005; Walsh et al., 2016). Indeed, as in marine sediments, the availability of electron acceptors decreased with increasing sediment depth (Nelson, 1997; Wurzbacher et al., 2017; Zhu et al., 2023), leading to depth‐related stratification in the composition of the prokaryotic community in freshwater sediments. Climatic conditions at the time of deposition of prokaryotic cells in sediments are expected to influence sedimentary geochemical conditions (Møller et al., 2020; Orsi et al., 2017), but microorganisms deposited on surface sediments and buried over time could further alter the geochemical characteristics and abundance of prokaryotic populations themselves (Thomas & Ariztegui, 2019; Vuillemin et al., 2013).…”