Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

Abstract

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

“…Betaproteobacteria, the dominant proteobacteria in the catotelm of the studied fen profile, were a minor group in some bogs. However, they constituted the second largest group of proteobacteria in the rock underlying bogs (at a depth of 650-700 cm) [20] and were the most widespread class among proteobacteria in bottom sediments [53]. Among the cultivated representatives of Betaproteobacteria in the fen profile under study, bacteria of different genera with various functions were identified.…”

“…Intermediate and rich fens, in contrast to bogs and poor fens, have an increased proportion of Bacteroidota [31]. Moreover, Bacteroidota, along with Proteobacteria and Acidobacteriota, was the main phyla in the microbiome of the bottom sediments [53]. In the studied fen profile, Bacteroidota was represented by the families Chitinophagaceae (35%-41%), Flavobacteriaceae (34%), or Cytophagaceae (35%) in the acrotelm and Sphingobacteriaceae (11%-36%), Chitinophagaceae (17%-28%), and env.OPS 17 (15%-27%) in the catotelm.…”