Microbial succession in biofilms growing on artificial substratum in subtropical freshwater aquaculture ponds

Abstract

Biofilms can be used to improve the water quality in aquaculture ponds, and elucidating the process of microbial succession in biofilms would allow the characterization of metabolic processes and permit optimization. In the present study, microbial succession of a biofilm growing on artificial substrata in a subtropical freshwater pond was investigated by high-throughput sequencing. Providing artificial substrata effectively reduced the concentrations of total nitrogen and total phosphorus in the pond. Relatively stable microbiota were formed after approximately 1 week. The dominant phyla in the mature biofilm were Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. The relative abundances of denitrifiers and phosphorus-removing bacteria, such as those in Comamonadaceae and Neisseriaceae, were significantly increased. The use of avermectin B1 changed the community structure of the microbiota; the microbiota were more similar to those at Week 0 than to those at Week 3. However, the microbial community structure recovered after approximately 1 week. Our results indicate that using artificial substrata can create a habitat for denitrifiers and phosphorus-removing bacteria, and thereby improve pond water quality. This study provided insight into how the use of artificial substrata could improve water quality and elucidated the environment-biofilm relationship in a subtropical freshwater pond.

Biofilm formed on different natural substrates enhances the growth and survival in Macrobrachium rosenbergii (de Man, 1879) juveniles

“…The lower levels of ammonia nitrogen in the treatment tanks may be due to the nitrification processes facilitated by the microbial biomass attached to the plant substratum in the tanks. Li et al (2017) also reported that the provision of artificial substrata effectively reduced the concentrations of total nitrogen in freshwater aquaculture pond.…”

Peer Review #1 of "Artificial substrata increase pond farming density of grass carp (Ctenopharyngodon idella) by increasing the bacteria that participate in nitrogen and phosphorus cycles in pond water (v0.1)"

“…Further, artificial substrata have been used in ponds to enhance the formation of biofilms that aid in controlling N and P (Li et al, 2014;Yu et al, 2016). Our previous study also showed that adding artificial substrata to an aquaculture pond could create a habitat for denitrifiers and phosphorus-removing bacteria (Li et al, 2017). In the present study, bacteria involved in N and P cycles such as Hyphomicrobium (Sperl & Hoare, 1971;van der Drift & de Windt, 1983;Brooke, Duchars & Attwood, 1987;Kloos et al, 1995), Chitinimonas (Chang et al, 2004), Legionella (Keen & Hoffman, 1984), Shewanella (Al-Harbi & Uddin, 2006;Hau & Gralnick, 2007;Fredrickson et al, 2008), Roseiflexus (Wawrik et al, 2011;Penton et al, 2013;Gerbl et al, 2014;Hug et al, 2015;Wang et al, 2018), and Planktothrix (Zotina, Köster & Jüttner, 2003;Davis et al, 2015) were enhanced on the artificial substrata and in associated pond water (Fig.…”

“…PCR was performed in 30-l reaction volumes with 15 l of Phusion High-Fidelity PCR Master Mix (New England Biolabs, Ipswich, MA, USA), each primer at 0.2 M, and approximately ng of template DNA. Thermal cycling conditions were as reported previously (Li et al, 2017). The PCR products were mixed at ratios of equal density and the mixed PCR products were purified using the Gene JET Gel Extraction Kit (Thermo Scientific, USA).…”

“…Introducing artificial substrata that improve microbial attachment can significantly promote the growth of aquaculture species while restoring water properties in situ (Bo et al, 2010;Audelo-Naranjo, Martínez-Córdova & Voltolina, 2010;Schveitzer et al, 2013;Kumar et al, 2015;Li et al, 2017). The main ways that artificial substrata promote fish growth include the following: reducing ammonia and nitrite concentrations in farming water through the assimilation and dissimilation of microorganisms that adhere to the surface of artificial substrata (Arndt et al, 2002;Zhang et al, 2019); providing natural feed to farming organisms through the presence of adherent microorganisms on the surface of artificial substrata, such as bacteria, fungi, algae, protozoa, and zooplankton (Azim et al, 2002); reducing energy consumption caused by stress reactions through the physical shelter provided by these structures (Huang et al, 2013;Pandey, Bharti & Kumar, 2014).…”

Peer Review #1 of "Epizootic ulcerative syndrome causes cutaneous dysbacteriosis in hybrid snakehead (Channa maculata♀ × Channa argus♂) (v0.1)"

“…PCR amplification was carried out using the prokaryotic primer set 515F (5-GTG CCA 148 GCM GCC GCG GTA A-3) and 806R (5-GGA CTA CHV GGG TWT CTA AT-3) for the V4 149 region of the 16S rRNA gene, as we have described previously (Tamaki et al, 2011;Li et al, 150 2016; Li et al, 2017;Ni et al, 2018). The resulting PCR products were pooled and purified using 151 an Axygen gel extraction kit (Axygen, USA).…”