Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal

Abstract

The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.

Intestinal Microbiota Differences in Litopenaeus vannamei Shrimp between Greenhouse and Aquaponic Rearing

“…According to the annotation of FaPROTAX, the YE group had significantly higher levels of photoheterotrophy, phototrophy, hydrocarbon degradation, thiosulfate respiration, and cellulolysis than those of the WE group, suggesting that these results are consistent with those of a aquaponic system that combined plants and biological floating biomass [ 43 ]. Previous studies found that methylotrophy is largely driven by the orders of Rhodobacterales and Rhodospirillales [ 44 ]. The WE group, which possessed higher light intensity than that of the YE group, displayed a significantly higher relative abundance of Rhodobacterales due to the higher levels of methylotrophy present.…”

Bacterial Metabolic Potential in Response to Climate Warming Alters the Decomposition Process of Aquatic Plant Litter—In Shallow Lake Mesocosms

“…Heterotrophic metabolism may also be limited by light, as we found that photoheterotrophic metabolic potential is abundant, especially in spring when they are significantly promoted by warming. Photoheterotrophs (rhodopsin-containing bacteria and aerobic anoxygenic phototrophs) harness solar energy to produce ATP but cover most of their energy requirements through respiration, not fixing inorganic [ 55 ]. This may be related to changes in bacterial communities of proteobacteria and actinobacteria in mesocosms.…”

Diversity, distribution, and expression of opsin genes in freshwater lakes

“…Opsin gene taxonomic diversity in freshwater has been previously studied (Atamna-Ismaeel et al . 2008; Galachyants et al . 2021; Martinez-Garcia et al .…”

“…Opsin gene taxonomic diversity in freshwater has been previously studied (Atamna-Ismaeel et al 2008;Galachyants et al 2021;Martinez-Garcia et al 2012;Sharma et al 2009). However, some of these studies were constrained by PCR primer limitations or difficulties for accurate phylogenetic inference when lacking closely related freshwater reference sequences.…”

“…In addition to ActR, opsin gene fragments were also recovered from a few other phyla in freshwater lakes (Atamna-Ismaeel et al . 2008; Galachyants et al . 2021; Martinez-Garcia et al .…”