Community structure of actively growing bacteria in a coastal fish-farming area

Abstract

In fish-farming areas, copious amounts of organic matter are released into the surrounding environment. Although it is well-known that bacterial community structures and activities are tightly coupled with organic conditions in the environment, actively growing bacteria (AGB) species that are responsible are still largely unknown. Here, we determined seasonal variations in the community structures of free-living and particle-attached AGB in surface and bottom seawater, and also in the easily resuspendable sediment boundary layer. Accordingly, we used bromodeoxyuridine (BrdU) magnetic bead immunocapture and PCR-denaturing gradient gel electrophoresis (BUMP-DGGE) analysis. Whereas overall bacterial communities in the resuspendable sediment were quite different from those of the free-living and particle-attached bacteria, the AGB community structures were similar among them. This result suggests that sediment resuspension in aquaculture environments functions as an organic source for bacteria in the water column, and that bacterial species contributing to the environmental capacity and carbon cycle are limited. We identified 25 AGB phylotypes, belonging to Alphaproteobacteria (Roseobacter clade, nine phylotypes), Gammaproteobacteria (five phylotypes), Deltaproteobacteria (one phylotype), Bacteroidetes (seven phylotypes), and Actinobacteria (three phylotypes). Among them, some AGB phylotypes appeared throughout the year with high frequency and were also identified in other coastal environments. This result suggests that these species are responsible for the environmental capacity and carbon cycle, and are key species in this fish-farming area, as well as other coastal environments.

Community Structure and Predicted Functions of Actively Growing Bacteria Responsive to Released Coral Mucus in Surrounding Seawater

“…The substrate to be labeled with the antibody may vary depending on the purpose of the analysis, and a phylogenetic analysis of AGB in soil and marine environments has been conducted using an immunocapture technique with antibody-conjugated magnetic beads. Previous studies demonstrated that community structures significantly differed between total bacteria and AGB (Taniguchi et al, 2011;Taniguchi and Eguchi, 2020), which is consistent with the present results showing that the observed ASVs were less abundant in actively growing microbes than in total microbes (Table 2). Similar findings were obtained in studies using an identical BrdU approach; however, these studies were not conducted in a coral envi- ronment and did not use MiSeq sequencing (Hamasaki et al, 2007;Taniguchi et al, 2015).…”

“…This result suggests that specific bacteria occur as AGB in certain seasons, namely, spring and autumn in the present study. Previous studies reported that bacterial community structures occur annually with repeatable temporal patterns ( Fuhrman et al , 2006 ; Chow et al , 2013 ) and that similar structures form between spring and autumn ( Mestre et al , 2020 ; Taniguchi and Eguchi, 2020 ). The factors affecting bacterial community structures are environmental and include water temperature, salinity, and inorganic nutrients ( Fuhrman et al , 2006 ; Mestre et al , 2020 ).…”

Effect of the probiotic Lactococcus lactis on the microbial composition in the water and the gut of freshwater prawn ( Macrobrachium rosenbergii ) cultivate in biofloc

“…It agrees with the present study, because the nitrogenous compounds were obtained in optimal values for the prawns. Finally, Actinobacteria have the capacity to degrade diverse polymers, such as cellulose, lignin and chitin (this last one is in the shell of the prawns) and for this reason it was obtained a better water quality in the probiotic treatments (Taniguchi & Eguchi, 2020).…”

“…However, when talking about biofloc systems it must be considered that the conditions to produce aquatic organisms differ significantly to conventional systems, because this type of systems promotes the growth of a very complex diversity of heterotrophic bacteria (Enterobacter, Bacillus, and Lactococcus) from an added carbon source and high oxygenation, which together with the cultured species influences, the bacterial groups that can resist certain conditions (Ray and Lotz, 2014;Wilén et al, 2008). Finally, Actinobacteria have the capacity to degrade diverse polymers, such as cellulose, lignin and chitin (this last one is in the shell of the prawns) and for this reason it was obtained a better water quality in the probiotic treatments (Taniguchi & Eguchi, 2020).…”

Targeted Cell Labeling and Sorting of Prokaryotes for Cultivation and Omics Approaches

“…Copper-free click chemistry has been widely used in a variety of biological projects [Baskin et al, 2007;Fugier et al, 2015;Cañeque et al, 2018;. Synthetic substrates used in click chemistry are commercially available in several different forms: synthetic substitutes of L-methionine (L-azidohomoalanine [AHA] and L-homopropargylglycine [HPG]), modifiable N-acetylmuramic acid derivatives (MurNAc, NAM [DeMeester et al, 2018;DeMeester et al, 2019]), lipopolysaccharide component analog 8-azido-8-deoxy-Kdo (8AzKdo [Wang et al, 2017a]) and thymidine analogs (5-bromo-2′-deoxyuridine [BrdU] and 5-ethynyl-2′-deoxyuridine [EdU] [Borneman, 1999;Tada and Grossart, 2014;Taniguchi and Eguchi, 2020]) are some examples. Natural substances, such as D-glutamic acid and D-alanine [Liang et al, 2017], as well as numerous forms of glycans [Li et al, 2020;Han et al, 2021], have also been used as labels due to their uniqueness in bacteria.…”