Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Abstract

Caves are typified by their permanent darkness and a shortage of nutrients. Consequently, bacteria play an important role in sustaining such subsurface ecosystems by dominating primary production and fueling biogeochemical cycles. China has one of the world’s largest areas of karst topography in the Yunnan-Guizhou Plateau, yet the bacteriomes in these karst caves remain unexplored. In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed. Results revealed abundant and diversified bacterial communities in karst caves, with Proteobacteria , Actinobacteria , and Firmicutes being the most abundant phyla. Statistical analysis revealed no significant difference in bacteriomes among the eight caves. However, a PCoA plot did show that the bacterial communities of 128 cave samples clustered into groups corresponding to sampling types (air, water, rock, and sediment). These results suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected. Further community-level composition analysis indicated that Proteobacteria were most dominant in water and air samples, while Actinobacteria dominated the sediment and rock samples. Co-occurrence analysis revealed highly modularized assembly patterns of the cave bacterial community, with Nitrosococcaceae wb1-P19, an uncultured group in Rokubacteriales , and an uncultured group in Gaiellales , being the top-three keystone members. These results not only expand our understanding of cave bacteriomes but also inspires functional exploration of bacterial strains in karst caves.

Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession

“…In the water samples collected in Panel Cave, Proteobacteria clearly dominated the microbiome (>21% of the total taxa), with either Bacteroidetes or Actinobacteria as the second most abundant (>5%). This is consistent with the aquatic bacterioplankton of 8 karst caves in the Yunnan-Guizhou Plateau of China ( Zhu et al, 2019 ). Also, Wu et al (2015) observed the phylum Nitrospira was more prominent inside the Jinjia Cave in the western Loess Plateau of China than in surface soils, which is consistent with our observations from water inside and outside of Panel Cave.…”

“…Different phyla appear to predominate, however, in the cave soil vs water microbiomes. In soil, Actinobacteria is the most abundant, followed by Proteobacteria ( Wu et al, 2015 ; Wisechart et al, 2018 , 2019 ; Thompson et al, 2019 ; Zhu et al, 2019 ). In the water samples collected in Panel Cave, Proteobacteria clearly dominated the microbiome (>21% of the total taxa), with either Bacteroidetes or Actinobacteria as the second most abundant (>5%).…”

“…When combined with deep-sequencing technologies, metabarcoding gives researchers the ability to screen millions of individual DNAs and identify thousands of unique sequences from an environmental sample ( Handelsman, 2004 ; Wooley, Godzik & Friedberg, 2010 ). To date, this technique has been used to survey microbes in cave soils, speleothems, water, and biofilms in temperate and extreme environments ( Ortiz et al, 2013 ; Wu et al, 2015 ; Lavoie et al, 2017 ; Pfendler et al, 2018 ; Wisechart et al, 2018 , 2019 ; Thompson et al, 2019 ; Burow et al, 2019 ; D’Angeli et al, 2019 ; Zhu et al, 2019 ; Dong et al, 2020 ).…”

Colored Microbial Coatings in Show Caves from the Galapagos Islands (Ecuador): First Microbiological Approach

“…The actinobacterial order Acidimicrobiales (which includes the Fe-reducer Aciditerrimonas) was present in anaerobic digesters [80], and soils [82][83][84]. Finally, Gaiellaceae (Gaiella) was found in limestone [40,85] and volcanic caves [13,37]. For Zhang et al [86] Gaiella is involved in the N cycle.…”

Distribution of Microbial Generalists and Habitat Specialists in Soils Along a Climate Gradient in the Chilean Coastal Cordillera

“…We identi ed Pyrinomonadales (RB41) as most dominant boundary-crossing specialist, which was recently shown to endure low-nutrient stress conditions, thereby playing an important role in maintaining the soil metabolic functions [99]. We further obtained several groups (Gemmatimonadaceae, Nitrosomonadaceae, Rokubacteriales, Gaiella) with previously described potential a nities for soil nitrate [100,101] and Streptomyces, which was recently correlated with their plant-growth promoting abilities by stimulating the mycorrhiza formation, thereby also improving the drought tolerance of plants [102].…”