Unrevealing variation of microbial communities and correlation with environmental variables in a full culture-cycle of Undaria pinnatifida

Highlights

• Undaria pinnatifida cultivation in the coastal ecosystem increased pH and dissolved oxygen.

• The temporally dynamics of microbial communities in seaweed cultivation areas were observed.

• Flavobacteriia and Thaumarchaeota increased and β-proteobacteria and Acidimirobiia decreased with the growth of seaweed.

• T, DO, pH and nitrogen were the major influencing factors of microbial communities during the U. pinnatifida aquaculture.

Abstract

Bacteria are the most abundant organisms in natural environment and dominant drivers of multiple geochemical functions. Drawing a global picture of microbial community structure and understanding their ecological status remain a grand challenge. As a typical artificial process, aquaculture provides a large amount of foods and creates great economic benefits for human beings. However, few studies are aimed at the microbial community in the aquaculture environment of aquatic plants. We analyzed microbial communities from 21 water samples in a coastal aquaculture area during the whole cultural process of Undaria pinnatifida by using high-throughout sequencing of 16S rRNA gene. The progression of U. pinnatifida aquaculture can be divided into three stages, named Seeding, Growth, and Maturity, respectively. Microbial community structures in water of the aquaculture area were significantly changed during the progression of U. pinnatifida aquaculture. The relative abundance of Flavobacteriia and Thaumarchaeota classes increased in Growth stage, and β-proteobacteria and Acidimirobiia classes decreased with the growth of U. pinnatifida. Meanwhile, environmental factors shaping the microbial community structures were uncovered during the U. pinnatifida aquaculture by using canonical correspondence analysis and Mantel test, in which temperature, dissolved oxygen, pH and nitrogen could be the major influencing factors. In addition, the microbial functions based on KEGG pathways were predicted from the microbial community compositions by PICRUSt. The comparison of predicted functions suggested that Environmental Information Processing and Genetic Information Processing were the functional categories with the most obvious shift in abundance among different stages of U. pinnatifida aquaculture. The findings of this study allowed us to better understand the microbial community in coastal aquaculture systems and the impact of seaweed cultivation on coastal ecosystems.

Introduction

Bacteria are the most abundant organisms on the earth and their cell numbers are 2–3 orders of magnitude higher than that of animals and plants in natural ecosystems. Bacteria are also dominant drivers for a variety of important geochemical functions, such as nutrient cycling (Fernandez et al., 2016; Li et al., 2016a, Li et al., 2016b), energy conversion (Kojima, 2015) and organic matter degradation (Liao et al., 2015; Repeta et al., 2016). In order to explore the disciplines of natural ecosystems, microbial community structures have been investigated in various environments, such as soils (Deangelis et al., 2015; Lange et al., 2015), rivers (Li et al., 2016a, Li et al., 2016b), groundwater (Nitzsche et al., 2015), air (Shin et al., 2015) and ocean (Lucas et al., 2015; Sun et al., 2015). Compared to natural environments, nowadays microbial communities in the environments affected by anthropogenic activities have received more attentions, including industrial (Yan et al., 2015), agricultural (Horemans et al., 2016), urban (Meynet et al., 2012), rural (Liu et al., 2013) and their wastes receiving environments (Guo et al., 2016; Ju and Zhang, 2015). To better understand the microbial communities influenced by anthropogenic activities and their regulatory factors could create a greater economic benefit for humans and maintain a better ecology balance of the earth. Therefore, it is necessary to clarify the influence of anthropogenic activities on microbial communities. However, drawing a global picture of microbial community structure and their function diversity remains a grand challenge (Sunagawa et al., 2015).

As a typical artificial process, aquaculture provides a large amount of foods for human beings and at the same time creates great economic benefits. With an enormous biomass, combined with high turnover rates and environmental complexity, aquaculture environments provide an extreme genetic diversity. In aquaculture environments, microorganisms have a wide variety of functions. Various pathogens, such as Vibrio splendidus (Zhang et al., 2006), Pseudomonas spp. (Xin et al., 2006) and Pseudoalteromonas tetraodonis (Liu et al., 2010), have been frequently observed from aquaculture environment. These pathogens resulted in the death of breeding species and caused enormous losses of this industry (Li et al., 2016a, Li et al., 2016b; Munang'Andu, 2016). Moreover, a variety of microorganisms have also been spotted that can promote the decomposition of residual feedstuffs, feces, and other organic substances (Hai, 2015; Dawood and Koshio, 2016; Tan et al., 2016). A variety of probiotic agents have also been widely used in aquaculture, such as Rhodococcus SM2 (Sharifuzzaman et al., 2017), Pseudomonas MCCB 102 and 103 (Preetha et al., 2015), and Bacillus (Gullian et al., 2004). The ability of these probiotics accelerates the circulation of nutrients and purifies water quality in aquaculture (Akhter et al., 2015). In addition, microorganisms in aquaculture environment can also convert harmful substances, such as ammonia, nitrite, and hydrogen sulfide, into low toxic substances (Su et al., 2016a,b). However, most of the previous studies on microorganisms in aquaculture were based on plate culture method to isolate probiotics or pathogens. In recent years, with the development of sequencing technology, more attentions have been paid to studies of microbial community structures in coastal sea farming aquaculture. The planktonic microbial communities have been analyzed at the coastal sea bass farm in the middle Adriatic sea to evaluate the their seasonal pattern changed by farming activity (Stefanija et al., 2016). Bacterial communities in sediments underneath milkfish cages and adjacent off-cage areas in Philippine Sea were characterized and the results indicated that bacterial composition was influenced by the organic load from the feed (Santander et al., 2016). Nevertheless, these studies were focused on aquatic animals breeding environments, and almost no studies aimed attention to the microbial community in aquaculture of aquatic plants.

Seaweed Undaria pinnatifida has long been exploited as one of the most valuable sea food due to its superior nutritive values (Jurković et al., 2010). Meanwhile, U. pinnatifida has very high medicinal properties, which can prevent hypertension and other human diseases (Synytsya et al., 2010). The aquaculture of U. pinnatifida had developed rapidly and became one of the most important aquaculture species in Asia (Sato et al., 2016). However, very few researches concerned at the microorganisms associated with U. pinnatifida, and most of these studies followed with interest in isolating bacterial strain to degrade U. pinnatifida (Kim et al., 2008; Tang et al., 2011). Two recent studies have focused on the effects of seaweed cultivation on microbial communities in culture areas and divergent microbial communities were observed between seaweed cultivation zones and non-aquaculture zones (Hu et al., 2017; Xie et al., 2017). However, there is not a clear understanding for the temporally dynamics of microbial communities in seaweed cultivation areas. The results of such studies can not only provide new insights into the effect of seaweed cultivation on microbial communities, but also well understand the interactions among seaweed processes, microbial communities and their environments in this coastal aquaculture system.

The progression of U. pinnatifida aquaculture can be divided into three stages. Firstly, the seedlings of U. pinnatifida are put into the aquaculture sea areas in September. Then, the base of U. pinnatifida generates rhizoids, which fix it on the surface of solid materials. This stage is named Seeding stage. Secondly, as the water temperature descending after November, the cultured U. pinnatifida get into the Growth stage. Finally, with the rise of water temperature in second year, the growth of U. pinnatifida slow down and reach maturity in March. This stage is named Maturity stage. High-throughput sequencing based on 16S rRNA genes was used in this study to investigate the microbial communities in a sea area during the whole process of U. pinnatifida aquaculture. The objects of this study are: 1) to draw the picture of microbial community variations during the progression of U. pinnatifida aquaculture; 2) to provide an overview of the core and different microbes among the different stages of U. pinnatifida aquaculture; 3) to explore the relationships between environmental factors and microbial community structures in U. pinnatifida aquaculture area. The results of this study could expand our understanding of the microbial communities associated with U. pinnatifida and will be benefit in exploiting the microbial agents or other techniques in the aquaculture of U. pinnatifida.