Dynamic change in bacterial communities in the integrated rice–fish farming system in Sleman, Yogyakarta, Indonesia

Abstract

An integrated rice-fish farming system is an efficient technique used to maintain water quality and rice/fish productivity. In addition to fish and rice plants that have mutually beneficial ecological roles, bacteria play important roles in maintaining water quality and soil fertility. Therefore, this study investigated the diversity and dynamic change in the bacterial community composition of water and sediment in an integrated ricefish farming system using a high-throughput sequencing approach. The 16S rRNA gene of bacteria was amplified, and the IonS5™XL sequencing platform was used to identify bacterial community during the cultivation period. The results demonstrated that fishpond, rice field and trench sediment samples were dominated by the phyla Proteobacteria (60.9%-64.4%), Acidobacteria (8.7%) and Chloroflexi (6.3%), whereas water samples were dominated by the phyla Proteobacteria (65.7%), Bacteroidetes (17.1%) and Actinobacteria (8.5%). The dynamics of the bacterial community composition of the water and sediment samples were clearly observed at phylum and genus levels respectively. Water temperature (34.67°C) and ammonia-nitrogen content (0.38 mg L −1 ) at the early stage of cultivation correlated with the abundances of Actinobacteia and Cyanobacteria at the phylum level and Acinetobacter at the genus level. Furthermore, several bacterial genera could potentially contribute to the biogeochemical cycle. In particular, Sorangium was involved in organic matter degradation, Methylophilus was implicated in nitrification, Novosphingobium and Methylotenera were essential for denitrification, and Desulfobacca was important for sulfate reduction. This study improved our understanding of the bacterial community in the integrated rice-fish farming system and provided data for further development.

Bacterial abundance and community composition in green, brown and red water from intensive catfish (Clarias sp.) culture ponds in Yogyakarta, Indonesia

“…The bacterial richness as Chao1 in this study was ranged from 1475.26 to 1331.71 (average 1394.9). In contrast, the bacterial community in pond of mina padi integrated culture was 1169.9 (Herlambang et al 2021), the semi-intensive aquaculture for European sea bass (Dicentrarchus labrax) was ranged from 216.53 to 1148.86 (Duarte et al 2019), the sediments from Chilean salmon aquaculture sites were ranged from 275.4 to 331.9 (Hornick and Buschmann 2018). The intensive catfish culture has put a lot of input such as the high nutrient of feed, so that the nutrient content of water is also high, giving possibility for many microorganisms to grow.…”

“…This study showed that the most dominant phylum in green and brown water samples was Proteobacteria. Other studies showed that Proteobacteria was also found as the most dominant phylum of bacterial communities in lakes (Kurilkina et al 2016;Huang et al 2017;Zhang et al 2019), river (Li et al 2008;Abia et al 2018), freshwater aquaculture (Fan et al 2015;Qin et al 2016), and minapadi field in India (Gupta 2020;Herlambang et al 2021), mariculture of European sea bass (Martins et al 2018;Duarte et al 2019). Proteobacteria exhibits diverse biochemical energy-generating mechanisms; some of its members are phototrophs (e.g., purple Chromatium, Rhodospirillum), or chemolithotrophs (e.g., sulfur-oxidizing bacteria, including Thiobacilli, and ammonia-oxidizing bacteria, such as Nitrosomonas), chemoorganotrophs (e.g., Escherichia coli) (Kersters et al 2006).…”

“…The second abundant green and brown water class was different as the Gammaproteobacteria (21.6%) and Alphaproteobacteria (14.3%), respectively. The minapadi system's water study showed that those three classes as Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria were the three most dominant classes (Herlambang et al 2021 (Martin et al 2018). The sampling events throughout the year of 2014 from aquaculture system showed that the most abundant bacterial classes were Gammaproteobacteria (41.73±4.71%), Flavobacteriia (20.79±7.26%), Alphaproteobacteria, (13.55±5.26%) (Duarte 2019).…”

Seasonal variations in microbial diversity and metabolite profiles of the gut of sea cucumber (Apostichopus japonicus)

“…From our analysis of intestinal microbial diversity across different seasons, we observed Proteobacteria maintained dominant positions. Proteobacteria is the largest bacterial flora population in aquaculture systems, and the most abundant phylum in the trench sediment and water samples (Herlambang et al, 2021). Thus, Proteobacteria of gut of A. japonicus may come from environment.…”

“…Previous studies have shown that, Proteobacteria is also dominant bacteria in sea urchin (Hakim et al, 2016), and this bacterium has major roles in nitrogen and carbon cycles in aquaculture environments (Wiegand et al, 2018). According to previous research on the rice-fish farming system which investigated the effects of several classes of Proteobacteria in nutrient cycle, such as, Alphaproteobacteria members are involved in the nitrogen cycle (Newton et al, 2011), Gammaproteobacteria help modulate excess nitrate (Fernandes et al, 2014;Herlambang et al, 2021). At the same time, this bacterium is related to sulfurrelated processes, from the study of metabolites, it can be found that the sulfur metabolism pathway is indeed subjected to some changes.…”