Metagenomic analysis shows diverse,distinct bacterial communities in biofilters among different marine recirculating aquaculture systems

While biofilters are widely used to metabolize ammonia and other metabolic waste products in recirculating aquaculture systems, their microbial communities are not thoroughly characterized. While inroads have been made characterizing microbial communities within single biofilters, replicated comparisons across biofilters and facilities have been lacking. We hypothesized that microbial communities might differ among filter types and facilities. We characterized and compared the bacterial communities of nine nitrification biofilters in five commercial recirculating marine aquaculture operations by amplifying and sequencing the 16S rRNA gene using the Illumina-MiSeq DNA sequencing platform. Our results demonstrated the usefulness of the approach for elucidating bacterial community structure in aquaculture biofilters; among almost 249,000 usable DNA sequence reads—a mean of 27,663 for each biofilter—we detected a mean of 682 operational taxonomic units. Higher species diversity was observed in the submerged biofilters at farms 3 and 4 (HF_SB1, HF_SB2, HF_SB3, MB_SB1, MB_SB2, and MB_SB3), and a bead filter at farm 2 (XYF-MBBR) than in a bead filter at farm 1 (DF_MBBR) and a fluidized sand filter at farm 5 (TY_FSF). At the phylum level, Proteobacteria were the most frequently observed taxa (representing 36–50 % of reads in the overall data set for a given filter); other frequently observed phyla were Bacteroidetes (13–34 %), Chloroflexi (2–23 %), Nitrospirae (1–7 %), Planctomycetes (1–4 %), and Actinobacteria (2–5 %). However, in fluidized sand filters, after Proteobacteria, the subdominant phyla were Bacteroidetes (19 %), Nitrospirae (17 %), and Planctomycetes (11 %). At the genus level, the nitrite-oxidizing genus Nitrospira was frequently observed in sand filter TY_FSF (16.4 %), bead filter DF_MBBR (7.6 %), submerged biofilter MB_SB1 (7 %), and bead filter XHF_MBBR (7.36), and less frequently in submerged biofilters HF_SB3 (1.94), HF_SB2 (1.77 %), and HF_SB1 (1.63 %), and bead filters MB_SB2 (0.8 %) and MB_SB1 (0.2 %). Observations of the ammonia-oxidizing genus Nitrosomonas varied widely within and among filter types, ranging from 0.06 % in submerged bed filter HF_SB3 to 2.82 % in bead filter DF_MBBR. Principal components and cluster analyses classified the bacterial communities in the nine biofilters into groups corresponding to the respective recirculating marine aquaculture operations and the associated filter types.     

Environmental factors on virulence of <Emphasis Type="Italic">Aeromonas hydrophila</Emphasis>

Aeromonas hydrophila are known for being opportunistic pathogens, harboring various virulence factors and triggering lesions and death in fish. The disease caused by bacteria can make fish inappropriate for human consumption, besides representing a risk to public health. The pathogenesis can be influenced by environmental variables, affecting fish productivity and mortality. The present study aimed to determine whether A. hydrophila harbor the virulence genes aerolysin, hydrolipase, elastase, lipase, cytotonic enterotoxin (ast), lateral flagellum (laf), and polar flagellum (fla) and to evaluate the influence of environmental variables on in vitro growth, in vivo virulence and expression of some of these genes. Polymerase chain reaction (PCR)-based screening for the presence of these virulence genes was performed on 35 isolates. Six isolates containing different profiles of virulence genes were tested for in vitro growth under different conditions of pH, temperature, and ammonia and for in vivo virulence under these same environmental conditions. RT-qPCR was used to quantify the expression of aerolysin, lipase, and fla genes. All the tested environmental factors influenced the growth of A. hydrophila, while pH and ammonia concentrations influenced the bacterial virulence. The expression of the fla gene increased when bacteria were grown in higher ammonia concentration. The mortality established by Aeromonas is influenced by several environmental factors pinpointing the importance of its control in fish farming to avoid higher economic loses associated to bacterial disease outbreaks.     

Long-term fluctuations in mollusk populations before and after the appearance of the alien predator <Emphasis Type="Italic">Euspira fortunei</Emphasis> on the Tona coast,Miyagi Prefecture,northern Japan

The impact of Euspira fortunei as an alien predator on fluctuations in population densities of prey mollusks between 2001 and 2010 on the Tona coast, northern Japan, was investigated. This species increased dramatically from 2002 to 2004. In contrast, prey species such as Ruditapes philippinarum and Macoma incongrua decreased rapidly from 2001 to 2004, whereas Pillucina pisidium and Batillaria cumingii did not show a significant decrease during this period. Using a laboratory experiment, we were able to show that these decreases in the population densities of some species of mollusks but not other species were the result of species-selective predation by E. fortunei, as the experiment revealed that E. fortunei preferred to attack R. philippinarum and M. incongrua rather than P. pisidium, although the predator did expand its diet to include P. pisidium after it had consumed 16 of the 20 preferred prey available (i.e., R. philippinarum and M. incongrua). This case study suggests that invasive naticid predators have the potential to affect the population density and community structure of prey mollusks in recipient coastal ecosystems through predation.     

Immunomodulatory effects of <Emphasis Type="Italic">Rhodomyrtus tomentosa</Emphasis> leaf extract and its derivative compound,rhodomyrtone, on head kidney macrophages of rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>)

Rhodomyrtus tomentosa is a medicinal plant that shows biological effects including immunomodulatory activity on human and other mammals but not in fish. In this study, we evaluated the in vitro immunomodulatory effects of R. tomentosa leaf extract and its active compound, rhodomyrtone, on the immune responses, using rainbow trout (Oncorhynchus mykiss) head kidney (HK) macrophages as a model. The tested immune functions included the expression of genes involved in innate immune and inflammatory responses and the production of reactive oxygen species (ROS). Gene expression was evaluated after exposure to 10 μg mL^?1 of R. tomentosa and 1 μg mL^?1 of rhodomyrtone for 4 and 24 h. R. tomentosa and rhodomyrtone induced changes in the expression of pro-inflammatory cytokines (il1β, il8, and tnfα), anti-inflammatory cytokines (il10 and tgfβ), inducible enzymes (inos, cox2, and arginase), and an antioxidant enzyme (gpx1). Co-exposure of R. tomentosa with LPS resulted in a prominent reduction in the expression of genes related to an inflammatory process (il1β, il8, tnfα, inos, saa, hepcidin, and gpx1), suggesting anti-inflammatory effects. Similarly, co-exposure of rhodomyrtone with LPS led to a downregulation of inflammation-related genes (il1β, inos, saa, and hepcidin). In addition, exposure to both natural plant products caused a reduction in cellular ROS levels by HK macrophages. The present results indicate that R. tomentosa and rhodomyrtone exerted immunostimulatory and anti-inflammatory effects on fish macrophages, thus opening up the possibility of using these natural products to further develop immunostimulants for health management in aquaculture.     

<Emphasis Type="Italic">Streptococcus agalactiae</Emphasis> from tilapia (<Emphasis Type="Italic">Oreochromis</Emphasis> sp.) transmitted to a new host,bighead carp (<Emphasis Type="Italic">Aristichthys nobilis</Emphasis>), in China

Several outbreaks of Streptococcus agalactiae infection of bighead carp (Aristichthys nobilis) were observed in China. The molecular epidemiology and pathogenicity of S. agalactiae in bighead carp and tilapia (Oreochromis sp.) is poorly understood. In the present study, we identified S. agalactiae strains isolated from diseased bighead carp using the API 20 Strep kit and 16S rDNA sequencing and determined whether these strains came from tilapia. Of the 46 identified S. agalactiae strains, 24 strains were successfully isolated from diseased bighead carps, 20 S. agalactiae strains were isolated from tilapia, and two S. agalactiae strains were isolated from tiger frog (Hoplobatrachus chinensis). The results of molecular typing, including multilocus sequence typing, molecular serotyping, surface protein gene detection, and virulence-related gene detection showed that the 44 strains from bighead carp and tilapia were highly similar, whereas different from tiger frog GBS strains. Remarkably, the bighead carp strain Hn1404 showed high virulence in bighead carp and zebrafish. Moreover, this strain was pathogenic to Nile tilapia (Oreochromis niloticus). In addition, comparative genomic analysis showed that isolate Hn1404 had a close relationship with the bighead carp and tilapia S. agalactiae strains. All the analyses of the genetic characteristics of bighead carp and tilapia strains showed that tilapia S. agalactiae strains could be transmitted to other fish species such as bighead carp.     

Dietary supplementation of curcumin augments heat stress tolerance through upregulation of <Emphasis Type="Italic">nrf-2</Emphasis>-mediated antioxidative enzymes and <Emphasis Type="Italic">hsps</Emphasis> in <Emphasis Type="Italic">Puntius sophore</Emphasis>

Heat stress is one of the major environmental concerns in global warming regime and rising temperature has resulted in mass mortalities of animals including fishes. Therefore, strategies for high temperature stress tolerance and ameliorating the effects of heat stress are being looked for. In an earlier study, we reported that Nrf-2 (nuclear factor E2-related factor 2) mediated upregulation of antioxidative enzymes and heat shock proteins (Hsps) provide survivability to fish under heat stress. In this study, we have evaluated the ameliorative potential of dietary curcumin, a potential Nrf-2 inducer in heat stressed cyprinid Puntius sophore. Fishes were fed with diet supplemented with 0.5, 1.0, and 1.5% curcumin at the rate 2% of body weight daily in three separate groups (n = 40 in each group) for 60 days. Fishes fed with basal diet (without curcumin) served as the control (n = 40). Critical thermal maxima (CTmax) was determined for all the groups (n = 10, in duplicates) after the feeding trial. Significant increase in the CTmax was observed in the group fed with 1.5% curcumin- supplemented fishes whereas it remained similar in groups fed with 0.5%, and 1% curcumin-supplemented diet, as compared to control. To understand the molecular mechanism of elevated thermotolerance in the 1.5% curcumin supplemented group, fishes were given a sub-lethal heat shock treatment (36 °C) for 6 h and expression analysis of nrf-2, keap-1, sod, catalase, gpx, and hsp27, hsp60, hsp70, hsp90, and hsp110 was carried out using RT-PCR. In the gill, expression of nrf-2, sod, catalase, gpx, and hsp60, hsp70, hsp90, and hsp110 was found to be elevated in the 1.5% curcumin-fed heat-shocked group compared to control and the basal diet-fed, heat-shocked fishes. Similarly, in the liver, upregulation in expression of nrf-2, sod, catalase, and hsp70 and hsp110 was observed in 1.5% curcumin supplemented and heat shocked group. Thus, this study showed that supplementation of curcumin augments tolerance to high temperature stress in P. sophore that could be attributed to nrf-2-induced upregulation of antioxidative enzymes sod, catalase, gpx, and the hsps.     

Gene expression of thyrotropin- and corticotrophin-releasing hormones is regulated by environmental salinity in the euryhaline teleost <Emphasis Type="Italic">Sparus aurata</Emphasis>

In euryhaline teleosts, the hypothalamus-pituitary-thyroid and hypothalamus-pituitary-interrenal axes (HPT and HPI, respectively) are regulated in response to environmental stimuli such as salinity changes. However, the molecular players participating in this physiological process in the gilthead seabream (Sparus aurata), a species of high value for aquaculture, are still not identified and/or fully characterized in terms of gene expression regulation. In this sense, this study identifies and isolates the thyrotropin-releasing hormone (trh) mRNA sequence from S. aurata, encoding prepro-Trh, the putative factor initiating the HPT cascade. In addition, the regulation of trh expression and of key brain genes in the HPI axis, i.e., corticotrophin-releasing hormone (crh) and corticotrophin-releasing hormone-binding protein (crhbp), was studied when the osmoregulatory status of S. aurata was challenged by exposure to different salinities. The deduced amino acid structure of trh showed 65–81% identity with its teleostean orthologs. Analysis of the tissue distribution of gene expression showed that trh mRNA is, though ubiquitously expressed, mainly found in brain. Subsequently, regulation of gene expression of trh, crh, and crhbp was characterized in fish acclimated to 5-, 15-, 40-, and 55-ppt salinities. In this regard, the brain gene expression pattern of trh mRNA was similar to that found for the crh gene, showing an upregulation of gene expression in seabream acclimated to the highest salinity tested. Conversely, crhbp did not change in any of the groups tested. Our results suggest that Trh and Crh play an important role in the acclimation of S. aurata to hypersaline environments.     

Medicinal plant extracts modulate respiratory burst and proliferation activity of rainbow trout (<Emphasis Type="Italic">Oncorhynchus mykiss</Emphasis>) leukocytes

The present study was designed to investigate the immunomodulatory effects of Aloe vera, Curcuma longa, Echinacea purpurea, Lavandula officinalis, Origanum vulgare, Panax ginseng, and Rheum officinale extracts on leukocytes purified from rainbow trout (Oncorhynchus mykiss) head kidney. The cells were cultured in a medium containing increasing doses of extracts; afterwards, they were tested for reactive oxygen species production after stimulation with phorbol myristate acetate (PMA) and proliferation in the presence or absence of phytohemagglutinin from Phaseolus vulgaris (PHA-P). After a 2-h exposure, the extracts of L. officinalis, O. vulgare, and R. officinale strongly reduced the oxidative burst activity of PMA-stimulated leukocytes, in a dose-dependent manner (P ≤ 0.05). A. vera, C. longa, E. purpurea, and P. ginseng extracts reduced this response with lower efficacy and especially at lower concentrations. On the contrary, the highest concentration of ginseng extract stimulated the respiratory burst of leukocytes compared to untreated control cells. After a 72-h exposure, the extracts of L. officinalis, R. officinale, C. longa, E. purpurea, and P. ginseng had a clear dose-dependent stimulatory effect on leukocyte proliferation (P ≤ 0.05). The results suggest that these medicinal plants can be considered as reliable sources of new antioxidants or immunostimulants to be used in aquaculture.     

Activity of metabolic enzymes and muscle-specific gene expression in parr and smolts Atlantic salmon <Emphasis Type="Italic">Salmo salar</Emphasis> L. of different age groups

This study was conducted to characterize the energy metabolism level and the features of muscle growth regulation during the development of Atlantic salmon (Salmo salar) inhabiting the Indera River (Kola Peninsula, Russia). The activities of aerobic and anaerobic enzymes (cytochrome c oxidase and lactate dehydrogenase) and carbohydrate metabolism enzymes (glucose-6-phosphate dehydrogenase, glycerol-3-phosphate dehydrogenase, and aldolase) were measured in muscle and liver tissue. Gene expression levels of myosin heavy chain (MyHC), myostatin (MSTN-1a), and myogenic regulatory factors (MRFs—MyoD1a, MyoD1b, MyoD1c, Myf5, myogenin) were measured in the white muscles of salmon parr of ages 0+, 1+, 2+, and 3+ and smolts of ages 2+ and 3+. Multidirectional changes in the activity of enzymes involved in aerobic and anaerobic energy metabolism with age were shown in the white muscles of the parr. The cytochrome c oxidase activity was higher in muscles of underyearlings (0+) and yearlings (1+) and decreased in 2+ and 3+ age groups. The activity of lactate dehydrogenase, in contrast, increased with age. The patterns of changes in expression levels of MyoD1a, MyoD1b, myogenin, MyHC, and MSTN-1a at different ages of the parr were similar. Particularly, the expression of these genes peaked in the yearling parr (1+) and then decreased in elder groups. The differences were revealed in parameters studied between the parr and smolts. The level of aerobic and anaerobic metabolism enzyme activities was higher in the white muscles of smolts than in parr. The activity of carbohydrate metabolism enzymes was decreased in the smolts’ livers. The expression levels of MyHC, MyoD1a, MyoD1b, and myogenin were lower in smolts at age 2+ compared to parr. These findings expand our knowledge of age-related and stage-related features of energy metabolism and muscle development regulation in young Atlantic salmon in their natural habitat. The results might be used for monitoring of the salmon population during restoration and rearing.     

Gene structure and expression analyses of multiple vitellogenesis-inhibiting hormones in the whiteleg shrimp <Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>

In the whiteleg shrimp Litopenaeus vannamei, the existence of six sinus gland peptides (SGPs) possessing vitellogenesis-inhibiting hormone (VIH) function has been previously demonstrated. Genomic and cDNA sequence information for two of these is already known. Here, we cloned cDNAs for the remaining three, i.e., those encoding Liv-SGP-A, -B, and -F. The deduced amino acid sequences were comprised of a signal peptide, a CHH precursor-related peptide, a mature peptide, and a C-terminal amidation signal. The genomic DNA for Liv-SGP-A, -B, -C, -F, and -G, was found to be organized as three exons and two introns. The insertion of the two introns were conserved in all VIH genes, with intron I being inserted six residues following the signal peptide, and intron II after the 40th residue of the mature peptide. We also quantified the relative simultaneous expression of Liv-SGP-A, -B, -C, -F, and -G in relation to molting and unilateral eyestalk ablation. The expression levels of each gene in the eyestalks of adults did not change significantly during molting or following unilateral eyestalk ablation. However, unilateral eyestalk ablation significantly decreased expression levels at 10 and 20 days for Liv-SGP-A and -C, and at 20 days for Liv-SGP-G in the eyestalks of subadults. This study has therefore clarified the genomic structure of the five major subtype I VIHs in L. vannamei, and elucidated their expression levels in the eyestalks in relation to molting and unilateral eyestalk ablation.     

Effect of growth hormone overexpression on gastric evacuation rate in coho salmon

Growth hormone (GH) transgenic (T) coho salmon consistently show remarkably enhanced growth associated with increased appetite and food consumption compared to non-transgenic wild-type (NT) coho salmon. To improve understanding of the mechanism by which GH overexpression mediates food intake and digestion in T fish, feed intake and gastric evacuation rate (over 7 days) were measured in size-matched T and NT coho salmon. T fish displayed greatly enhanced feed intake levels (~ 2.5-fold), and more than 3-fold increase in gastric evacuation rates relative to NT coho salmon. Despite the differences in feed intake, no differences were noted in the time taken from first ingestion of food to stomach evacuation between genotypes. These results indicate that enhanced feed intake is coupled with an overall increased processing rate to enhance energy intake by T fish. To further investigate the molecular basis of these responses, we examined the messenger RNA (mRNA) levels of several genes in appetite- and gastric-regulation pathways (Agrp1, Bbs, Cart, Cck, Glp, Ghrelin, Grp, Leptin, Mc4r, Npy, and Pomc) by qPCR analyses in the brain (hypothalamus, preoptic area) and pituitary, and in peripheral tissues associated with digestion (liver, stomach, intestine, and adipose tissue). Significant increases in mRNA levels were found for Agrp1 in the preoptic area (POA) of the brain, and Grp and Pomc in pituitary for T coho salmon relative to NT. Mch and Npy showed significantly lower mRNA levels than NT fish in all brain tissues examined across all time-points after feeding. Mc4r and Cart for T showed significantly lower mRNA levels than NT in the POA and hypothalamus, respectively. In the case of peripheral tissues, T fish had lower mRNA levels of Glp and Leptin than NT fish in the intestine and adipose tissue, respectively. Grp, Cck, Bbs, Glp, and Leptin in stomach, adipose tissue, and/or intestine showed significant differences across the time-points after feeding, but Ghrelin showed no significant difference between T and NT fish in all tested tissues.     

New insights into the evolution,hormonal regulation,and spatiotemporal expression profiles of genes involved in the Gfra1/Gdnf and Kit/Kitlg regulatory pathways in rainbow trout testis

The present study aimed to investigate whether the Gfra1/Gdnf and/or Kit/Kitlg regulatory pathways could be involved in the regulation of spermatogonial cell proliferation and/or differentiation in fish. Homologs of the mammalian gfra1, gdnf, kitr, and kitlg genes were identified in gnathostomes and reliable orthologous relationships were established using phylogenetic reconstructions and analyses of syntenic chromosomal fragments. Gene duplications and losses occurred specifically in teleost fish and members of the Salmoninae family including rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Some duplicated genes exhibited distinct spatiotemporal expression profiles and were differently regulated by hormones in rainbow trout. Undifferentiated type A spermatogonia expressed higher levels of kitrb and kitra2 making them possible target cells for the gonadal kitlgb and somatic kitlga before the onset of spermatogenesis. Interestingly, gdnfa and gdnfb ohnologous genes were poorly expressed before the onset of spermatogenesis. The expression level of gdnfb was correlated with that of the vasa gene suggesting that the late increased abundance of gdnfb during spermatogenesis onset was due to the increased number of spermatogonial cells. gfra1a2 was expressed in undifferentiated type A spermatogonia whereas gfra1a1 was mainly detected in somatic cells. These observations indicate that the germinal gdnfb ligand could exert autocrine and paracrine functions on spermatogonia and on testicular somatic cells, respectively. Fsh and androgens inhibited gfra1a2 and gdnfb whereas gfra1a1 was stimulated by Fsh, androgens, and 17α, 20β progesterone. Finally, our data provide evidences that the molecular identity of the male germ stem cells changes during ontogenesis prior to spermatogenesis onset.     

Diethylstilbestrol arrested spermatogenesis and somatic growth in the juveniles of yellow catfish (<Emphasis Type="Italic">Pelteobagrus fulvidraco</Emphasis>), a fish with sexual dimorphic growth

In fish, spermatogenesis and somatic growth are mainly regulated by hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-somatic (HPS) axes, respectively. Xenoestrogens have been reported to impair spermatogenesis in some fishes, and arrest somatic growth in some others, whereas, whether xenoestrogens are capable of disrupting spermatogenesis and somatic growth simultaneously in fish that exhibits sexual dimorphic growth is little known, and the underlying mechanisms remain poorly understood. In this study, male juveniles of yellow catfish (Pelteobagrus fulvidraco), which exhibits a sexual dimorphic growth that favors males, were exposed to diethylstilbestrol (DES) for 28 days. After exposure, DES significantly disrupted the spermatogenesis (decreased gonadal-somatic index (GSI) and germ cell number) and arrested the somatic growth (declined body weight) of the catfish juveniles. Gene expression and plasma steroid analyses demonstrated the suppressed mRNA levels of genes in HPG axis (gnrh-II, fshβ, and lhβ in the brain and dmrt1, sf1, fshr, cyp17a1, cyp19a1a, and cyp11b2 in the testis) and decreased 17β-estrodial (E2) and 11-ketotestosterone (11-KT) levels in plasma. Further analysis revealed the arrested germ cell proliferation (cyclin d1), meiosis (dmc1, sycp3), and enhanced apoptosis (decreased bcl-2 and elevated bax/bcl-2 ratio) in the testis. Besides, DES also suppressed the mRNA levels of genes in HPS axis (ghrh, gh, and prl in the brain and ghr, igf1, igf2a, and igf2b in the liver). The suppressed HPG and HPS axes were thus supposed to disturb spermatogenesis and arrest somatic growth in yellow catfish. The present study greatly extended our understanding on the mechanisms underlying the toxicity of DES on spermatogenesis and somatic growth of fish.     

Seasonal expression of arginine vasotocin mRNA and its correlations to gonadal steroidogenic enzymes and sexually dimorphic coloration during sex reversal in the gilthead seabream (<Emphasis Type="Italic">Sparus aurata</Emphasis>)

Arginine vasotocin is a hormone produced in the hypothalamus of teleost fish that has been shown to regulate gonad development and sexual behavior. To study the role of arginine vasotocin in the gonadal cycle of the hermaphrodite gilthead seabream, Sparus aurata, we cloned the seabream arginine vasotocin (avt) complementary DNA (cDNA). We investigated the expression of brain avt throughout the gonad cycle using real-time quantitative PCR and compared its expression levels to the expression levels of two key gonadal steroidogenic enzymes, cyp19a1a and cyp11b2. In July, when the process of sex reversal is thought to begin, avt expression was elevated over the previous 2 months. Avt in the brain remained at or above the level of July until November then peaked again in December. There was no difference between males and females in the expression levels of brain avt throughout the year. However, only in ambisexual fish was the expression of the cyp19a1a gonadal aromatase correlated to the expression of avt in the brain. Cyp11b2 did not show any correlation to brain avt expression. We also found that females had more intense body coloration than males and that this intensity peaked prior to spawning. Avt expression and female coloration were positively correlated. The fact that brain avt expression was lowest during gonad quiescence, together with the observation of a correlation between brain avt with gonadal cyp19a1a and body coloration during that time suggests that avt may play a role during the process of sex reversal and spawning of the gilthead seabream.     

Metabolic and phylogenetic profiles of microbial communities from a mariculture base on the Chinese Guangdong coast

This study examined the phylogenetic and metabolic features of microbial communities in Baisha Bay mariculture areas of Nan’ao Island, a mariculture base on the Chinese Guangdong coast. Large seaweed (Gracilaria lemaneiformis) cultivation zones (LZ), fish culture zones (FZ), and control zones (CZ) were sampled. According to community-level physiological profiling, d-mannitol, d-mannitol/α-d-lactose, and d-mannitol/α-cyclodextrin were the carbon sources with the highest utilization rates in CZ, LZ, and FZ, respectively (R _s  > 1.9). Denaturing gradient gel electrophoresis analysis showed that the dominant bacteria in CZ and LZ were Alphaproteobacteria (39.9 and 34.5%, respectively), whereas in FZ they were Flavobacteria (32.2%). The Shannon diversity in CZ and LZ was significantly higher than in FZ (P < 0.05). Some opportunistic pathogens, such as Vibrio, Pseudoalteromonas and Loktanella, were abundant in FZ. The microbial communities and most of the dominant bacteria in FZ were more affected by environmental factors including salinity, chemical oxygen demand and total phosphorus. Some bacteria, such as Brevundimonas and Polaribater, have the potential to degrade agar in seaweed, and were isolated from samples rich in algae which are dominant in LZ. The cultivation of G. lemaneiformis created the notable structures and functions of macroalgae-associated bacterial communities that were less affected by the environmental factors examined.