Characterization of the bacterial community composition in a hypoxic zone induced by Microcystis blooms in Lake Taihu, China

Assessment of the performance of a symbiotic microalgal-bacterial granular sludge reactor for the removal of nitrogen and organic carbon from dairy wastewater

Cheese whey (CW) is a nutrient deficient dairy effluent, which requires external nutrient supplementation for aerobic treatment. CW, supplemented with ammonia, can be treated using aerobic granular sludge (AGS) in a sequencing batch reactor (SBR). AGS are aggregates of microbial origin that do not coagulate under reduced hydrodynamic shear and settle significantly faster than activated sludge flocs. However, granular instability, slow granulation start-up, high energy consumption and CO2 emission have been reported as the main limitations in bacterial AGS-SBR. Algal-bacterial granular systems have shown be an innovative alternative to improve these limitations. Unfortunately, algal-bacterial granular systems for the treatment of wastewaters with higher organic loads such as CW have been poorly studied. In this study, an algal-bacterial granular system implemented in a SBR (SBRAB) for the aerobic treatment of ammonia-supplemented CW wastewaters was investigated and compared with a bacterial granular reactor (SBRB). Mass balances were used to estimate carbon and nitrogen (N) assimilation, nitrification and denitrification in both set-ups. SBRB exhibited COD and ammonia removal of 100% and 94% respectively, high nitrification (89%) and simultaneous nitrification-denitrification (SND) of 23% leading to an inorganic N removal of 30%. The efficient algal-bacterial symbiosis in granular systems completely removed COD and ammonia (100%) present in the dairy wastewater. SBRAB microalgae growth could reduce about 20% of the CO2 emissions produced by bacterial oxidation of organic compounds according to estimates based on synthesis reactions of bacterial and algal biomass, in which the amount of assimilated N determined by mass balance was taken into account. A lower nitrification (75%) and minor loss of N by denitrifying activity (<5% Ng, SND 2%) was also encountered in SBRAB as a result of its higher biomass production, which could be used for the generation of value-added products such as biofertilizers and biostimulants.

Indole-3-acetic acid promotes growth in bloom-forming Microcystis via an antioxidant response

Interactions between bacteria and phytoplankton in the phycosphere facilitate and constrain biogeochemical cycling in aquatic ecosystems. Indole-3-acetic acid (IAA) is a bacterially produced chemical signal that promotes growth of phytoplankton and plants. Here, we explored the impact of IAA on bloom-forming cyanobacteria and their associated bacteria. Exposure to IAA and its precursor, tryptophan, resulted in a strong growth response in a bloom of the freshwater cyanobacterium, Microcystis. Metatranscriptome analysis revealed the induction of an antioxidant response in Microcystis upon exposure to IAA, potentially allowing populations to increase photosynthetic rate and overcome internally generated reactive oxygen. Our data reveal that co-occurring bacteria within the phycosphere microbiome exhibit a division of labor for supportive functions, such as nutrient mineralization and transport, vitamin synthesis, and reactive oxygen neutralization. These complex dynamics within the Microcystis phycosphere microbiome are an example of interactions within a microenvironment that can have ecosystem-scale consequences.

Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China

Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.

The decomposition of algae has a greater impact on heavy metal transformation in freshwater lake sediments than that of macrophytes

Heavy metal (HM) pollution is a major concern in freshwater ecosystem management. The different types of endogenous organic matter and the way their decomposition affects HM transformation in freshwater lakes is not well understood. An ex situ mesocosm study was conducted to compare HM transformation in sediments during anaerobic decomposition of cyanobacterial bloom biomass (CBB) and submerged cyanobacterial vegetation in Lake Taihu, known as Potamogeton malaianus (PM). Microbial community structures were examined through Illumina sequencing of 16S rDNA. Results indicate that Zn had a remarkably higher amount of potential mobile fraction than other heavy metals (Cr, Pb, Cu, Ni, and Cd) detected in sediments, especially in sediments collected from CBB-dominated areas (approximately 150 mg kg-1). CBB decomposition has caused a significant increase in exchangeable Zn content in sediments and a decrease in reducible Zn that was three times greater than PM decomposition. Additionally, oxidizable Zn content declined during CBB decomposition but increased during PM decomposition. Furthermore, the relative abundance of the main fermentative bacteria and some sulfate-reducing bacteria genera (e.g., Desulfomicrobium) were significantly associated with the HM content of exchangeable and reducible fractions during CBB decomposition. Overall, the findings indicate that Zn is more susceptible to endogenous organic matter decomposition than other metals in freshwater lakes, and the impacts of CBB decomposition on the transformation of heavy metals in sediment are greater than that of submerged macrophyte decomposition.

Eutrophication control of large shallow lakes in China

Large shallow lake refers to a polymictic system that is often well mixed without stratification during summer. Similar to a small and deep lake, a large and shallow lake has a high nutrient retention rate. Differing from a small and deep lake, it has an extensive sediment-water interface and internal loading from sediment, which has led to high susceptibility to eutrophication. There are many large and shallow freshwater lakes in the middle and lower Yangtze River (MLYR), China, experienced eutrophication and cyanobacteria blooms. To address this issue, a variety of methods focused on in-lake physical and biogeochemical processes was explored. The main gains of these studies included: (1) shallow lakes in the floodplain of the Yangtze River are prone to eutrophication because of their high trophic conditions; (2) wind-induced waves determine sediment resuspension, downward dissolved oxygen penetration, and upward soluble reactive nutrient mobilization, while wind-driven currents regulate the spatial distribution of water quality metrics and algal blooms; (3) the low P loss of shallow lakes via sedimentation and high N loss via denitrification lead to a low N:P ratio and N and P colimitation, which demonstrated the significance of dual N and P reduction for eutrophication control in shallow lakes; (4) extensive submerged macrophyte could suppress internal loading in large, shallow waters, but nutrient loading must be reduced and water clarity must be increased; and (5) climate warming promotes cyanobacterial blooms through positive feedback to exacerbate eutrophication in shallow lakes. The lack of action to address the challenges of non-point source pollution and internal loading from the sediment has led to limited effectiveness of eutrophication control in large shallow lakes under climate warming. In the future, the management of large shallow eutrophic lakes in China must combine social sciences (economic development) with natural technology (pollution reduction) to achieve sustainability.

Gene expression pattern of microbes associated with large cyanobacterial colonies for a whole year in Lake Taihu

Large cyanobacterial colonies, which are unique niches for heterotrophic bacteria, are vital for blooming in eutrophic waters. However, the seasonal dynamics of molecular insights into microbes in these colonies remain unclear. Here, the community composition and metabolism pattern of microbes inhabiting large cyanobacterial colonies (> 120 µm, collected from Lake Taihu in China) were investigated monthly. The community structure of total microbes was mostly influenced by chlorophyll a (Chl a), total phosphorus (TP) concentration, dissolved oxygen, and temperature, whereas the colony-associated bacteria (excluding Cyanobacteria) were mostly influenced by total organic carbon, NO₃^-, and PO₄^3- concentrations, indicating different response patterns of Cyanobacteria and the associated bacteria to water nutrient conditions. Metatranscriptomic data suggested that similar to that of Cyanobacteria, the gene expression patterns of the most active bacteria, such as Proteobacteria and Bacteroidetes, were not strictly dependent on season but separated by Chl a concentrations. Samples in July and September (high-bloom period) and February and March (non-bloom period) formed two distinct clusters, whereas those of other months (low-bloom period) clustered together. The accumulation of transcripts for pathways, such as phycobilisome from Cyanobacteria and bacterial chemotaxis and flagellum, phosphate metabolism, and sulfur oxidation from Proteobacteria, was enriched in high- and low-bloom periods than in non-bloom period. Network analyses revealed that Cyanobacteria and Proteobacteria exhibited coordinated transcriptional patterns in almost all divided modules. Modules had Cyanobacteria-dominated hub gene were positively correlated with temperature, Chl a, total dissolved phosphorus, and NH₄⁺ and NO₂^- concentrations, whereas modules had Proteobacteria-dominated hub gene were positively correlated with TP and PO₄^3-. These results indicated labor division might exist in the colonies. This study provided metabolic insights into microbes in large cyanobacterial colonies and would support the understanding and management of the year-round cyanobacterial blooms.

Microbial compositions, ecological networks, and metabolomics in sediments of black-odour water in Dongguan, China

Black-odour water with organic compounds and heavy metals caused by domestic and industrial activities has aroused people's attention in recent years, yet little is known about the ecological effects on aquatic organisms, especially microorganisms in sediments. To explore the response of microbial communities to environmental factors, the community and metabolites of nine river sediments with different pollution in Dongguan city, China were investigated using 16S rRNA gene sequencing and liquid chromatography tandem-mass. The results revealed that the composition and structure of sedimentary microbial communities significantly changed in rivers with varying pollution levels. Cyanobacteria were the most abundant organisms in the sediment of black-odorous rivers, while the relative abundance of Thaumarchaeota was gradually increased with the river quality gets better. The relative abundance of organic acids (including amino acids), alcohols, esters, and ketones associated with microbial metabolism in sediments of polluted rivers was increased. The 16S rRNA gene sequencing-based molecular ecological network analysis indicated that the interactions amongst bacteria were enhanced in severely contaminated communities. Sphingomonadaceae and Cyanobacteria have important roles in bacterial community structures of polluted rivers and those with ongoing treatment. The correlation analysis showed significant metal resistance and/or tolerance of the following bacteria species Thalassiosira weissflogii, Aminicenantes bacterium clone OPB95, 'Candidatus Halomonas phosphatis', and archaeal species Methanolinea and unidentified Thermoplasmata. These results indicated that sedimentary microbial communities may shift in composition and structure, as well as their interaction network, to adapt and resist environmental contamination and promote restoration.

Black blooms-induced adaptive responses of sulfate reduction bacteria in a shallow freshwater lake

Decomposing cyanobacterial bloom-induced black blooms been seen as an issue in the management of freshwater ecosystems, but its effect on sulfate-reducing bacteria (SRB) in shallow freshwater lakes is not clear. The objective of this study is to present an in-depth investigation of black bloom effects on the activities and composition of SRB, as well as the interactions between SRB and other bacteria. Water and surface sediments samples were collected from a shallow freshwater lake during black and non-black blooms. Sulfate reduction rates (SRRs) in the water column were determined from the linear regression of sulfate depletion with time. Quantitative real-time polymerase chain reactions (qPCRs), targeting the dsrA gene and Illumina sequencing of 16S rDNA, were used to estimate the SRB population and SRB community structures, respectively. Our data indicate that although a higher abundance of SRB was responsible for the higher SRR in the bottom water (34.09 ± 2.37 nmol mL^-1 day^-1) than in the surface water (14.57 ± 2.91 nmol mL^-1 day^-1) during black blooms, cell-specific sulfate reduction rates (csSRRs) in the distinct water layers were not significantly different (P = 0.95), with the value of approximately 0.017 fmol cell^-1 day^-1. Additionally, Desulfomicrobium and Desulfovibrio were the two main genera of SRB in the water column during black bloom season, while Desulfobulbus, Desulfobacca and Desulfatiglans genera were identified in the sediments of both the black and non-black blooms in genera pools. Each SRB genus preferentially associated with bacteria for specific functions in the bacterial co-occurrence network, regardless of whether black booms occurred or not. These results extend our knowledge on the importance of SRB during black blooms and the adaptation of SRB to environmental changes in freshwater lakes.

Insight into variations of DOM fractions in different latitudinal rural black-odor waterbodies of eastern China using fluorescence spectroscopy coupled with structure equation model

The structural compositions of dissolved organic matter (DOM) could profoundly affect formation and evolution of black-odor waterbodies (BOWs). In this study, 81 samples of BOWs were collected from three different latitudinal rural regions in eastern China, including low, middle and high latitude regions. Based on fluorescence index (FI) and biological index (BIX) deduced from excitation-emission matrices (EEMs) of rural BOWs, biological source of DOM was dominant in low latitude, while DOM derived from both biological and terrestrial in mid-latitude and high-latitude. Furthermore, humification degree of DOM in the former was lower than those in the latter based on humification index (HIX) deduced from EEMs. Seven fluorescence components of DOM were extracted by EEMs combined with parallel factor analysis: components 1 and 2 (C1 and C2) known as tryptophan-like substances, C3 and C4 associated with tyrosine-like, C5 related with biological byproducts, C6 relative to fulvic-like, and C7 referred as humic-like. The roughly decreasing order of percentages in DOM fractions from the rural BOWs was tyrosine-like > tryptophan-like > fulvic-like > microbial byproduct > humic-like in three regions. According to hierarchical cluster analysis and redundancy analysis, the autochthonous fresh DOM was dominant in low latitudinal rural BOWs, which was relative to actions of phytoplankton and microorganisms. However, humification degree of DOM increased with a rise in latitude, which could attribute to variations of climate and agriculture industrial structure. Based on structure equation model, the C5 and FI were the potential factors of the rural BOWs, which suggested that microbial activity and pollution sources should affect formation and evolution of rural BOWs. These findings are conductive to reveal composition and fluorescence properties of DOM and in recognizing the potential factors of forming mechanism in rural BOWs, which could provide basic theoretical support for policymakers to regulate and treat it.

Evolution of urban black and odorous water: The characteristics of microbial community and driving-factors

Urban black blooms that are primarily caused by organic carbon are deleterious environmental problems. However, detailed studies on the microbial characteristics that form urban black blooms are lacking. In this study, we observed the composition, diversity, and function of bacterial community in the overlying water and sediments during the occurrence and remediation of urban black blooms using high-throughput 16S rRNA gene amplicon sequencing analysis. First, we found that pivotal consortia in the overlying water increased significantly during the formation of black blooms, including the genera Acidovorax, Brevundimonas, Pusillimonas, and Burkholderiales involved in the degradation of refractory organics, as well as the genera Desulfovibrio, Dechloromonas, and Rhizobium related to the production of black and odorous substances. An RDA analysis revealed that chemical oxygen demand, dissolved oxygen, and oxidation reduction potential were related to the changes in microbial community composition. Furthermore, aeration was found to accelerate the removal of ammonia nitrogen and enhance the function of microbial community by stimulating the growth of order Planktomycetes during the remediation of black blooms, but aeration substantially damaged the microbial diversity and richness. Therefore, the health of the aquatic ecosystem should be comprehensively considered when aeration is applied to restore polluted waterbodies. Notably, we observed a large number of pathogenic bacteria in urban black blooms, which emphasizes the importance of treating domestic sewage so that it is harmless. Together, these findings provide new insights and a basis to prevent and manage urban black blooms.

Cyanobacterial community succession and associated cyanotoxin production in hypereutrophic and eutrophic freshwaters

Cyanobacterial harmful algal blooms (cyanoHABs) in freshwater bodies are mainly attributed to excess loading of nutrients [nitrogen (N) and phosphorus (P)]. This study provides a comprehensive review of how the existing nutrient (i.e., N and P) conditions and microbial ecological factors affect cyanobacterial community succession and cyanotoxin production in freshwaters. Different eutrophic scenarios (i.e., hypereutrophic vs. eutrophic conditions) in the presence of (i) high levels of N and P, (ii) a relatively high level of P but a low level of N, and (iii) a relatively high level of N but a low level of P, are discussed in association with cyanobacterial community succession and cyanotoxin production. The seasonal cyanobacterial community succession is mostly regulated by temperature in hypereutrophic freshwaters, where both temperature and nitrogen fixation play a critical role in eutrophic freshwaters. While the early cyanoHAB mitigation strategies focus on reducing P from water bodies, many more studies show that both N and P have a profound contribution to cyanobacterial blooms and toxin production. The availability of N often shapes the structure of the cyanobacterial community (e.g., the relative abundance of N₂-fixing and non-N₂-fixing cyanobacterial genera) and is positively linked to the levels of microcystin. Ecological aspects of cyanotoxin production and release, related functional genes, and corresponding nutrient and environmental conditions are also elucidated. Research perspectives on cyanoHABs and cyanobacterial community succession are discussed and presented with respect to the following: (i) role of internal nutrients and their species, (ii) P- and N-based control vs. solely P-based control of cyanoHABs, and (iii) molecular investigations and prediction of cyanotoxin production.

Convergent community structure of algal-bacterial consortia and its effects on advanced wastewater treatment and biomass production

Microalgal-bacterial consortium is an effective way to meet increasingly stringent standards in wastewater treatment. However, the mechanism of wastewater removal effect has not been properly explained in community structure by phycosphere. And little is known about that the concept of macroecology was introduced into phycosphere to explain the phenomenon. In the study, the algal-bacterial consortia with different ratios of algae and sludge were cultured in same aerobic wastewater within 48 h in photobioreactors (PSBRs). Community structure at start and end was texted by metagenomic analysis. Bray-Curtis similarities analysis based on microbial community showed that there was obvious convergent succession in all consortia, which is well known as "convergence" in macroecology. The result showed that Bray-Curtis similarities at End (overall above 0.88) were higher than these at Start (almost less than 0.66). In terms of community structure, the consortium with 5:1 ratio at Start are the more similar with the consortia at End by which the maximum removal of total dissolved nitrogen (TDN, 73.69%), total dissolved phosphorus (TDP, 94.40%) and NH3-N (93.26%) in wastewater treatment process and biomass production (98.2%) higher than other consortia, according with climax community in macroecology with the highest resource utilization than other communities. Therefore, the macroecology can be introduced into phycosphere to explain the consortium for advanced wastewater treatment and optimization community structure. And the study revealed a novel insight into treatment effect and community structure of algal-bacterial consortia for advanced wastewater treatment, a new idea for to shortening the culture time of consortium and optimize predicting their ecological community structure and predicting ecological community.

High-resolution distribution of internal phosphorus release by the influence of harmful algal blooms (HABs) in Lake Taihu

The Mechanisms driving phosphorus (P) release in sediment of shallow lakes is essential for managing harmful algal blooms (HABs). Accordingly, this study conducted field monitoring of labile P, iron (Fe), sulfur (S), and dissolved manganese (Mn) in different biomass of algae in Lake Taihu. The in-situ technique of ZrO-Chelex-AgI (ZrO-CA) diffusive gradients in thin-films (DGT) and high-resolution dialysis sampler (high resolution-Peeper (HR-Peeper)) were used to measure labile P, Fe, S, and dissolved Mn, as well as their apparent diffusion fluxes at the sediment-water interface (SWI). In addition, the distribution of iron-reducing bacteria (IRB) and sulfate-reducing bacteria (SRB) in sediments was also detected. Results showed that high HABs biomass promoted the reduction of sulfate into labile S, however, IRB is the dominant species. Thus, labile Fe concentrations greatly exceeded labile S concentrations across all sites, indicating that microbial iron reduction (MIR) is the principal pathway for ferric iron reduction. Furthermore, the simple relationship analysis revealed the principal influence P migration and transformation is the Fe-P in high algal biomass sites, while Fe and Mn redox reactions did not significantly influence labile P mobilization in low algal areas.

Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia - a biogeographical study on Lake Remoray (France)

Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.

Advances in the use of microalgal-bacterial consortia for wastewater treatment: Community structures, interactions, economic resource reclamation, and study techniques

The rise in living standards has generated a demand for higher aquatic environmental quality. The microalgal community and the surrounding organic molecules, environmental factors, and microorganisms, such as bacteria, are together defined as the phycosphere. The bacteria in the phycosphere can form consortia with microalgae through various forms of interaction. The study of the species in these consortia and their relative proportions is of great significance in determining the species and strains of stable algae that can be used in sewage treatment. This article summarizes the following topics: the interactions between microalgae and bacteria that are required to establish consortia; how symbiosis between algae and bacteria is established; microalgal competition with bacteria through inhibition and anti-inhibition strategies; the influence of environmental factors on microalgal-bacterial aggregates, such as illumination conditions, pH, dissolved oxygen, temperature, and nutrient levels; the application of algal-bacterial aggregates to enhance biomass production and nutrient reuse; and techniques for studying the community structure and interactions of algal-bacterial consortia, such as microscopy, flow cytometry, and omics. PRACTITIONER POINTS: Community structures in microalgal-bacterial consortia in wastewater treatment. Interactions between algae and bacteria in wastewater treatment. Effects of ecological factors on the algal-bacterial community in wastewater treatment. Economically recycling resources from algal-bacterial consortia based on wastewater. Technologies for studying microalgal-bacterial consortia in wastewater treatment.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Conditions that promote the formation of black bloom in aquatic microcosms and its effects on sediment bacteria related to iron and sulfur cycling

Black bloom occurs frequently in eutrophic waters. We investigated the conditions promoted the formation of black bloom via in-situ measurement in two aquatic microcosms and the effects of black bloom on the bacterial community composition. Although larger changes in dissolved oxygen (DO) were detected in the Hydrilla verticillata-dominated microcosm over the 90-day simulation, black bloom occurred more readily in the phytoplankton-dominated than macrophyte-dominated microcosm under conditions of O₂ depletion and temperature above 30 °C. The sediment bacterial community composition shifted after black bloom; the relative abundance of Thiobacillus and Sideroxydans, which oxidize iron (Fe) and sulfur (S), decreased by 47% and 48%, respectively, in the phytoplankton-dominated microcosm and by 18% and 20% in the macrophyte-dominated microcosm. By contrast, Desulfatiglans increased by 13% and 19%, respectively, after black bloom. Furthermore, inter-taxa correlations remarkably changed according to co-occurrence network analysis. Thirty-six different taxa from the phylum to the genus level were identified as biomarkers of sediments collected before and after the black bloom event. Most of these biomarkers are related to Fe/S cycling in aquatic ecosystems.

Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove

Anthropogenic nutrient enrichment results in hypoxia, ocean acidification and elevated nutrients (HOAN) in coastal environments throughout the world. Here, we examined the composition of biofilm bacterial communities from a nutrient-excessive fish farm with low dissolved oxygen (DO) and pH levels using 16S rRNA gene sequencing. HOAN was accompanied by higher bacterial diversity and richness, and resulted in an altered community composition than the control site. HOAN resulted in more Flavobacteriales, Rhizobiales, Epsilonproteobacteria and Vibrionales, but less Oceanospirillales and Alteromonadales. Photobacterium sp. and Vibrio sp. were mostly found to be exclusive to HOAN conditions, suggesting that HOAN could possibly proliferate the presence of these potential pathogens. Our study suggests the complexity of bacterial communities to hypoxia and acidification in response to increased nutrient loads, along with identities of nutrient, oxygen and pH-susceptible bacterial groups that are most likely affected under this ocean trend.

The nitrogen reduction in eutrophic water column driven by Microcystis blooms

During the bloom seasons, the dissolved inorganic nitrogen declines, which results in the occurrence of nitrogen limitation. It is unclear where the nitrogen goes. Our enclosure experiments and batch tests suggested that Microcystis blooms could significantly reduce the nitrogen in water bodies and the key mechanisms for the nitrogen reduction in different layers were different. The assimilation was the main pathway for nitrogen reduction in the surface layer, while denitrification played an important role both at the sediment-water interface and in the overlying water. Stable nitrogen isotope experiments showed that the nitrate reduction efficiency at sediment-water interface was enhanced by Microcystis, reaching to 76.5∼84.7 %. Dissimilation accounted for 63.8∼67.3 % of the nitrate reduction, and the denitrification rate was 7.4∼8.5 times of DNRA rate. In the water column, the Microcystis bloom facilitated the formation of dark/anoxic condition, which favored the denitrification. The Microcystis aggregates collected from the field showed a great potential in removing nitrogen, and the TN in the overly water was reduced by 3.76∼6.03 mg L^-1 within two days. This study provided field evidences and deeper insights into the relationship between Microcystis blooms and nitrogen reduction in the whole water column and gave more details about the enhancing effects of Microcystis on nitrogen reduction.

A critical review of the appearance of black-odorous waterbodies in China and treatment methods

Black-odorous rivers and lakes are a serious environmental problem and are frequently reported in China. Despite this, there have been no comprehensive in-depth reviews of black-odorous water formation mechanisms, contributing factors and potential treatment technologies. Elements such as S, C and N play an important role in the biogeochemical cycle of black-odorous waterbodies, with water blackening caused by metal sulfides such as iron sulfide (FeS) and manganese sulfide (MnS). Volatile substances such as volatile organic sulfur compounds (VOSCs) are the main contributors of odor. Microorganisms such as sulfate reducing bacteria (SRB), Bacteroidetes and Proteobacteria play important roles in blackening and odor formation processes. Effectiveness of the commonly used treatments methods for black-odorous waterbodies, such as artificial aeration, sediment dredging, microbial enhanced technologies and constructed wetlands, varies significantly under different conditions. In contrast, bio-ecological engineering technologies exhibit comprehensive, long-lasting and economical treatment effects. The causes and mechanisms of black-odorous water formation require further investigation, as well as the optimal application conditions and mechanisms of treatment technologies. This study comprehensively reviews 1) the characteristics and current distribution of black-odorous waterbodies; 2) the compounds contributing to black-odorous phenomenon; 3) black-odorous waterbody production mechanisms; 4) treatment technologies for black-odorous waterbodies. Further studies on the mechanisms of blackening and odor formation are required, with treatment application conditions and mechanisms also requiring further clarification. In addition, the long-term ecological restoration of black-odorous rivers immediately after remediation is key issue that is easily overlooked but merits further investigation and development.

A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom

Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of MTB. We propose that deltaproteobacterial MTB may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment

Microcystis biomass remineralization after blooming represents a hotspot of nutrient recycling in eutrophic lakes. Because Microcystis blooms are massively deposited on lake sediments, resulting in anoxic conditions, it is important to understand the response and role of benthic microbial communities during the anoxic decomposition of Microcystis in freshwater lakes. In the present study, we employed a microcosm method, combined with high-throughput sequencing, functional prediction, and network analysis, to investigate microbial succession during the short-term (30 days) anaerobic decomposition of Microcystis in a eutrophic sediment. Continuous accumulation of CH4 and CO2 and increasing relative abundance of methanogens were observed during the incubation. The microbial community composition (MCC) significantly changed after addition of Microcystis biomass, with a shift in the community from a stochastic to a functional, deterministic succession. Families, including Clostridiaceae, Rhodocyclaceae, Rikenellaceae, Peptostreptococcaceae, Syntrophomonadaceae, Lachnospiraceae, and Methanosarcinaceae, were predominantly enriched and formed diverse substitution patterns, suggesting a synergistic action of these family members in the decomposition of Microcystis biomass. Importantly, intense species-to-species interactions and weak resistance to disturbance were observed in the microbial community after Microcystis biomass addition. Collectively, these results suggest that the addition of Microcystis induce phylogenetic clustering and structure instability in the sediment microbial community and the synergistic interactions among saprotrophic bacteria play a key role in Microcystis biomass remineralization.

Variations of bacterial community during the decomposition of Microcystis under different temperatures and biomass

BACKGROUND

The decomposition of Microcystis can dramatically change the physicochemical properties of freshwater ecosystems. Bacteria play an important role in decomposing organic matters and accelerating the cycling of materials within freshwater lakes. However, actions of the bacterial community are greatly influenced by temperature and the amount of organic matter available to decompose during a bloom. Therefore, it is vital to understand how different temperatures and biomass levels affect the bacterial community during the decomposition of Microcystis.

RESULTS

Microcystis addition reduced the diversity of bacterial community. The composition of bacterial community differed markedly between samples with different biomass of Microcystis (no addition, low biomass addition: 0.17 g/L, and high biomass addition: 0.33 g/L). In contrast, temperature factor did not contribute much to the different bacterial community composition. Total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), ammonia nitrogen (NH₄⁺-N) and oxidation-reduction potential (ORP) were the key measured environmental variables shaping the composition of bacterial community.

CONCLUSIONS

Decomposition of Microcystis changed the physicochemical characteristics of the water and controlled the diversity and composition of the bacterial community. Microcystis biomass rather than temperature was the dominant factor affecting the diversity and composition of the bacterial community.

Linking heterotrophic bacterioplankton community composition to the optical dynamics of dissolved organic matter in a large eutrophic Chinese lake

Elucidation of the linkages between the bacterial community composition and chromophoric dissolved organic matter (CDOM) in lake ecosystems is critical for the understanding of the inland water carbon cycling. Despite substantial research into the relationship between the bacteria community and the bulk DOM pool, knowledge of the specific relationship between the optical dynamics of DOM and the bacterioplankton community in lake ecosystems is still poor. We investigated the linkages between the optical dynamics of DOM and bacteria composition in shallow eutrophic Lake Taihu, China. Redundancy Analysis (RDA) indicated that besides water temperature and phytoplankton biomass, also CDOM was an important factor determining the composition of the bacterial community. Generalized Additive Models (GAM) showed that terrestrial humic-like C1 and tyrosine-like C4 were the key factors explaining the abundance of the main bacterial clades. C1 was closely correlated with Verrucomicrobia, Actinobacteria, Alphaproteobacteria, Betaproteobacteria and Planctomycetes, and C4 was closely related to the latter two and to Bacteroidetes. At family level, the dominant families - Pelagibacteraceae (Alphaproteobacteria) and Gemmataceae (Planctomycetes) - were related to both allochthonous and autochthonous CDOM fluorophores but responded differently to the various CDOM components. Tryptophan-like C2 was significantly and positively correlated with Gemmataceae and Ellin6075 (Acidobacteria). Additionally, we found that the biomasses of Cyanophyta, terrestrial humic-like C1, tryptophan-like C4 and C5 were significantly related to the richness of heterotrophic bacterioplankton. Our results provide new insight into the relationship between bacteria and DOM optical dynamics although the mechanisms leading to these relationships need further experimental investigations.

Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary

Bacterioplankton play a key role in the global cycling of elements. To characterize the effects of hypoxia on bacterioplankton, bacterial community structure and function were investigated in the Changjiang Estuary. Water samples were collected from three layers (surface, middle, and bottom) at ten sampling sites in the Changjiang Estuary hypoxic and non-hypoxic zones. The community structure was analyzed using high-throughput sequencing of 16S rDNA genes, and the predictive metagenomic approach was used to investigate the functions of the bacterial community. Co-occurrence networks are constructed to investigate the relationship between different bacterioplankton. The results showed that community composition in hypoxic and non-hypoxic zones were markedly different. The diversity and richness of bacterial communities in the bottom layer (hypoxic zone) were remarkably higher than that of the surface layer (non-hypoxic). In the non-hypoxic zone, it was found that Proteobacteria, Bacteroidetes, and Flavobacteriia were the dominant groups while Alphaproteobacteria, SAR406 and Deltaproteobacteria were the dominant groups in the hypoxic zone. From the RDA analysis, it was shown that dissolved oxygen (DO) explained most of the bacterial community variation in the redundancy analysis targeting only hypoxia zones, whereas nutrients and salinity explained most of the variation across all samples in the Changjiang Estuary. To understand the genes involved in nitrogen metabolism, an analysis of the oxidation state of nitrogen was performed. The results showed that the bacterial community in the surface layer (non-hypoxic) had more genes involved in dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, and anammox, while that in the middle and bottom layers (hypoxic zone) had more abundant genes associated with nitrogen fixation and nitrification. Co-occurrence networks revealed that microbial assemblages in the middle and bottom layers shared more niche spaces than in the surface layer (non-hypoxic zone). The environmental heterogeneity in the hypoxic and non-hypoxic zones might be important environmental factors that determine the bacterial composition in these two zones.

Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake

While the important roles of microbial communities in oceanic hypoxic zones were beginning to be understood, little is known about microbial community associated with this phenomenon in shallow lakes. To address this deficit, both the bacterial and microbial eukaryotic communities of an ephemeral hypoxic area of Taihu Lake were characterized. The hypoxia provided nutritional niches for various bacteria, which results in high abundance and diversity. Specific bacterial groups, such as vadinBC27 subgroup of Bacteroidetes, Burkholderiales, Rhodocyclales, Pseudomonas, and Parcubacteria, were dominated in hypoxic sites and relevant to the fermentation, denitrification, nitrification, and sulfur metabolism. Conversely, most of microbial eukaryotes disappeared along with the decline of DO. An unexpected dominance of fungi was observed during hypoxia, which partly explained by the accumulation of toxic algae. Mucor was the single dominant genus in the hypoxic zone. We proposed that this group might cooperate with bacterial communities in the anaerobic degradation of algal biomass and woody materials. Generally, the hypoxic microbiome in shallow lakes is mainly involved in fermentative metabolism depending on phytodetritus and is potentially influenced by terrestrial sources. This study provided new insights into the unique microbiome in short-term hypoxia in shallow lakes and lays the foundation for studies that will enhance our understanding of the microbial players associated with hypoxia and their adaption strategy on the global scale.

Temporal dynamics of microbiota before and after host death

The habitats that animals, humans and plants provide for microbial communities are inevitably transient, changing drastically when these hosts die. Because microbes associated with living hosts are ensured prime access to the deceased host’s organic matter, it is feasible that opportunistic, adaptable lifestyles are widespread among host-associated microbes. Here we investigate the temporal dynamics of microbiota by starving to death a host—the planktonic Crustacean Daphnia magna—and tracking the changes in its microbial community as it approaches death, dies and decomposes. Along with obligate host-associated microbes that vanished after the host’s death and decomposers that appeared after the host’s death, we also detected microbes with opportunistic lifestyles, seemingly capable of exploiting the host even before its death. We suggest that the period around host death plays an important role for host–microbiota ecology and for the evolution of hosts and their microbes.

Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm

Cyanobacterial blooms are a worldwide environmental problem and frequently occur in eutrophic lakes. Organophosphorus mineralization regulated by microbial alkaline phosphatase provides available nutrients for bloom regeneration. To uncover the dynamics of bacterial alkaline phosphatase activity and microbial backgrounds in relation to organophosphorus mineralization during the decomposition process of cyanobacterial blooms, the response of alkaline phosphatase PhoX-producing bacteria were explored using a 23-day mesocosm experiment with three varying densities of Microcystis biomass from eutrophic Lake Taihu. Our study found large amounts of soluble reactive phosphorus and dissolved organophosphorus were released into the lake water during the decomposition process. Bacterial alkaline phosphatase activity showed the peak values during days 5~7 in groups with different chlorophyll-a densities, and then all decreased dramatically to their initial experimental levels during the last stage of decomposition. Bacterial phoX abundances in the three experimental groups increased significantly along with the decomposition process, positively related to the dissolved organic carbon and organophosphorus released by the Microcystis blooms. The genotypes similar to the phoX genes of Alphaproteobacteria were dominant in all groups, whereas the genotypes most similar to the phoX genes of Betaproteobacteria and Cyanobacteria were also abundant in the low density (~15 μg L-1 chlorophyll-a) group. At the end of the decomposition process, the number of genotypes most similar to the phoX of Betaproteobacteria and Cyanobacteria increased in the medium (~150 μg L-1 chlorophyll-a) and high (~1500 μg L-1 chlorophyll-a) density groups. The released organophosphorus and increased bacterial phoX abundance after decomposition of Microcystis aggregates could potentially provide sufficient nutrients and biological conditions for algal proliferation and are probably related to the regeneration of Microcystis blooms in eutrophic lakes.

Large buoyant particles dominated by cyanobacterial colonies harbor distinct bacterial communities from small suspended particles and free-living bacteria in the water column

Worldwide cyanobacterial blooms greatly impair ecosystems in many eutrophic lakes and impact the microbial environment. In particular, large cyanobacterial colonies that are buoyant on the water surface may provide a distinct habitat for bacteria from other small particles that are suspended stably in the water column. To test this hypothesis, bacterial communities (excluding cyanobacteria) attached to large particles dominated by cyanobacterial colonies (>120 μm, LA), small particles (3–36 μm, SA), and free‐living bacteria (0.2–3 μm, FL) were investigated monthly for a year in Lake Taihu, China. Results confirmed that the Shannon diversity index of LA was significantly lower than that of FL, which was lower than that of SA. Cytophagia and Alphaproteobacteria were specially enriched in LA. Although samples in each habitat collected during high‐ (May to November) and low‐bloom seasons (December to April) were separated, all samples in LA were clustered and separated from SA and FL, which were also clustered during the same sampling seasons. In addition, the bacterial communities in LA were correlated with nitrate level, whereas FL and SA were correlated with nitrate level and temperature. Mantel analysis revealed that bacterial composition significantly correlated with the cyanobacterial composition in LA and FL but not in SA. These results indicate that LA provides distinct niches to bacteria, whereas the differentiation of bacterial communities in FL and SA is seasonally dependent.

Characterising and predicting cyanobacterial blooms in an 8-year amplicon sequencing time course

Cyanobacterial blooms occur in lakes worldwide, producing toxins that pose a serious public health threat. Eutrophication caused by human activities and warmer temperatures both contribute to blooms, but it is still difficult to predict precisely when and where blooms will occur. One reason that prediction is so difficult is that blooms can be caused by different species or genera of cyanobacteria, which may interact with other bacteria and respond to a variety of environmental cues. Here we used a deep 16S amplicon sequencing approach to profile the bacterial community in eutrophic Lake Champlain over time, to characterise the composition and repeatability of cyanobacterial blooms, and to determine the potential for blooms to be predicted based on time course sequence data. Our analysis, based on 135 samples between 2006 and 2013, spans multiple bloom events. We found that bloom events significantly alter the bacterial community without reducing overall diversity, suggesting that a distinct microbial community-including non-cyanobacteria-prospers during the bloom. We also observed that the community changes cyclically over the course of a year, with a repeatable pattern from year to year. This suggests that, in principle, bloom events are predictable. We used probabilistic assemblages of OTUs to characterise the bloom-associated community, and to classify samples into bloom or non-bloom categories, achieving up to 92% classification accuracy (86% after excluding cyanobacterial sequences). Finally, using symbolic regression, we were able to predict the start date of a bloom with 78-92% accuracy (depending on the data used for model training), and found that sequence data was a better predictor than environmental variables.

Variation of bacterial communities in water and sediments during the decomposition of Microcystis biomass

The bacterial community composition in water and sediment samples during the decomposition of Microcystis biomass were analyzed using the 454 pyrosequencing technique. We found dramatic shifts in the bacterial community composition of water and sediments after the addition of Microcystis biomass. Among all the detected phyla, only Firmicutes was found to be dominant in both water and sediment samples. The genus Clostridium sensu stricto was the absolutely dominant group in Firmicutes and showed drastic variations with incubation time during the decomposition process. Peak values in relative abundance of Clostridium sensu stricto appeared in the first few days for water and sediment samples. Environmental factors such as pH, dissolved oxygen (DO), and dissolved organic carbon (DOC) in water samples showed drastic variations during the decomposing process, which might be the prominent forces driving the variation of bacterial communities. The abundant genus, Clostridium sensu stricto, were thought to be well adapted to higher DOC and turbidity and lower pH and DO conditions. Compared with the sediment samples, the decomposition of Microcystis biomass had greater influence on the bacterial community composition in water and Clostridium sensu stricto might play important roles in the process of Microcystis biomass decomposition.

Relationship of Microbiota and Cyanobacterial Secondary Metabolites in Planktothricoides-Dominated Bloom

The identification of phytoplankton species and microbial biodiversity is necessary to assess water ecosystem health and the quality of water resources. We investigated the short-term (2 days) vertical and diel variations in bacterial community structure and microbially derived secondary metabolites during a cyanobacterial bloom that emerged in a highly urbanized tropical reservoir. The waterbody was largely dominated by the cyanobacteria Planktothricoides spp., together with the Synechococcus, Pseudanabaena, Prochlorothrix, and Limnothrix. Spatial differences (i.e., water depth) rather than temporal differences (i.e., day versus night) better-explained the short-term variability in water quality parameters and bacterial community composition. Difference in bacterial structure suggested a resource-driven distribution pattern for the community. We found that the freshwater bacterial community associated with cyanobacterial blooms is largely conserved at the phylum level, with Proteobacteria (β-proteobateria), Bacteroidetes, and Actinobacteria as the main taxa despite the cyanobacterial species present and geographical (Asia, Europe, Australia, and North America) or climatic distinctions. Through multivariate statistical analyses of the bacterial community, environmental parameters, and secondary metabolite concentrations, we observed positive relationships between the occurrences of cyanobacterial groups and off-flavor compounds (2-methyisoborneol and β-ionone), suggesting a cyanobacterial origin. This study demonstrates the potential of 16S rRNA gene amplicon sequencing as a supporting tool in algal bloom monitoring or water-resource management.

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.

Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea)

Over the past century the spread of hypoxia in the Baltic Sea has been drastic, reaching its ‘arm’ into the easternmost sub-basin, the Gulf of Finland. The hydrographic and climatological properties of the gulf offer a broad suite of discrete niches for microbial communities. The current study explores spatiotemporal dynamics of bacterioplankton community in the Gulf of Finland using massively parallel sequencing of 16S rRNA fragments obtained by amplifying community DNA from spring to autumn period. The presence of redoxcline and drastic seasonal changes make spatiotemporal dynamics of bacterioplankton community composition (BCC) and abundances in such estuary remarkably complex. To the best of our knowledge, this is the first study that analyses spatiotemporal dynamics of BCC in relation to phytoplankton bloom throughout the water column (and redoxcline), not only at the surface layer. We conclude that capability to survive (or benefit from) shifts between oxic and hypoxic conditions is vital adaptation for bacteria to thrive in such environments. Our results contribute to the understanding of emerging patterns in BCCs that occupy hydrographically similar estuaries dispersed all over the world, and we suggest the presence of a global redox- and salinity-driven metacommunity. These results have important implications for understanding long-term ecological and biogeochemical impacts of hypoxia expansion in the Baltic Sea (and similar ecosystems), as well as global biogeography of bacteria specialized inhabiting similar ecosystems.

The Vertical Distribution of Sediment Archaeal Community in the "Black Bloom" Disturbing Zhushan Bay of Lake Taihu

Using the Illumina sequencing technology, we investigated the vertical distribution of archaeal community in the sediment of Zhushan Bay of Lake Taihu, where the black bloom frequently occurred in summer. Overall, the Miscellaneous Crenarchaeotal Group (MCG), Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), and Methanobacterium dominated the archaeal community. However, we observed significant difference in composition of archaeal community among different depths of the sediment. DHVEG-6 dominated in the surface layer (0–3 cm) sediment. Methanobacterium was the dominating archaeal taxa in the L2 (3–6 cm) and L3 (6–10) sediment. MCG was most abundant in the L4 (10–15 cm) and L5 (15–20 cm) sediment. Besides, DHVEG-6 was significantly affected by the concentration of total phosphorus (TP). And loss on ignition (LOI) was an important environmental factor for Methanobacterium. As the typical archaeal taxa in the surface layer sediment, DHVEG-6 and Methanobacterium might be more adapted to abundant substrate supply from cyanobacterial blooms and take active part in the biomass transformation. We propose that DHVEG-6 and Methanobacterium could be the key archaeal taxa correlated with the “black bloom” formation in Zhushan Bay.

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

The frequency of freshwater cyanobacterial blooms is at risk of increasing as a consequence of climate change and eutrophication of waterways. It is increasingly apparent that abiotic data are insufficient to explain variability within the cyanobacterial community, with biotic factors such as heterotrophic bacterioplankton, viruses and protists emerging as critical drivers. During the Australian summer of 2012-2013, a bloom that occurred in a shallow ephemeral lake over a 6-month period was comprised of 22 distinct cyanobacteria, including Microcystis, Dolichospermum, Oscillatoria and Sphaerospermopsis. Cyanobacterial cell densities, bacterial community composition and abiotic parameters were assessed over this period. Alpha-diversity indices and multivariate analysis were successful at differentiating three distinct bloom phases and the contribution of abiotic parameters to each. Network analysis, assessing correlations between biotic and abiotic variables, reproduced these phases and assessed the relative importance of both abiotic and biotic factors. Variables possessing elevated betweeness centrality included temperature, sodium and operational taxonomic units belonging to the phyla Verrucomicrobia, Planctomyces, Bacteroidetes and Actinobacteria. Species-specific associations between cyanobacteria and bacterioplankton, including the free-living Actinobacteria acI, Bacteroidetes, Betaproteobacteria and Verrucomicrobia, were also identified. We concluded that changes in the abundance and nature of freshwater cyanobacteria are associated with changes in the diversity and composition of lake bacterioplankton. Given this, an increase in the frequency of cyanobacteria blooms has the potential to alter nutrient cycling and contribute to long-term functional perturbation of freshwater systems.

Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus

The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing) and Microcystis (colonial and non-N2 fixing) that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.

Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu

Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis.

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients

The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments.

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics

Algal blooms are a worldwide phenomenon and the biological interactions that underlie their regulation are only just beginning to be understood. It is established that algal microorganisms associate with many other ubiquitous, oceanic organisms, but the interactions that lead to the dynamics of bloom formation are currently unknown. To address this gap, we used network approaches to investigate the association patterns among microeukaryotes and bacterioplankton in response to a natural Scrippsiella trochoidea bloom. This is the first study to apply network approaches to bloom dynamics. To this end, terminal restriction fragment (T-RF) length polymorphism analysis showed dramatic changes in community compositions of microeukaryotes and bacterioplankton over the blooming period. A variance ratio test revealed significant positive overall associations both within and between microeukaryotic and bacterioplankton communities. An association network generated from significant correlations between T-RFs revealed that S. trochoidea had few connections to other microeukaryotes and bacterioplankton and was placed on the edge. This lack of connectivity allowed for the S. trochoidea sub-network to break off from the overall network. These results allowed us to propose a conceptual model for explaining how changes in microbial associations regulate the dynamics of an algal bloom. In addition, key T-RFs were screened by principal components analysis, correlation coefficients, and network analysis. Dominant T-RFs were then identified through 18S and 16S rRNA gene clone libraries. Results showed that microeukaryotes clustered predominantly with Dinophyceae and Perkinsea while the majority of bacterioplankton identified were Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. The ecologi-cal roles of both were discussed in the context of these findings.

Dissolved organic carbon and relationship with bacterioplankton community composition in 3 lake regions of Lake Taihu, China

To clarify the relationships between dissolved organic carbon (DOC) and bacterioplankton community composition (BCC), a 1-year survey (June 2009 - May 2010) was conducted in 3 regions of Lake Taihu (Meiliang Bay, Lake Center, and Eastern Taihu), China. Polymerase chain reaction - denaturing gradient gel electrophoresis was used to analyze the composition and heterogeneity of the bacterioplankton community. Canonical correspondence analysis was used to explore the relationships between DOC concentration and BCC. We found a significant negative correlation between DOC concentration and bacterioplankton community diversity (as measured by the Shannon-Wiener index (H')). The results show that spatial variation in the bacterioplankton population was stronger than the seasonal variation and that DOC concentration influences BCC in Lake Taihu. DOC concentration, followed by macrophyte biomass, water turbidity, and phytoplankton biomass were the most influential factors that account for BCC changes in Lake Taihu. More detailed studies on the relationship between DOC concentration and BCC should focus on differences in DOC concentrations and quality among these lake regions. DOC had a significant impact on BCC in Meiliang Bay. The relationship between DOC and BCC in the 2 other regions studied (Lake Center and Eastern Taihu) was weaker. The results of this study add to our understanding of the BCC in eutrophic lakes, especially regarding the role of the microbial loop in lake ecosystems.

Paenibacillus taihuensis sp. nov., isolated from an eutrophic lake

Two Gram-stain-negative, facultatively anaerobic and endospore-forming rod-shaped bacterial strains, THMBG22T and R24, were isolated from decomposing algal scum. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to each other (99.7 % similarity) and that they were also closely related to Paenibacillus sacheonensis DSM 23054T (97–97.1 %) and Paenibacillus phyllosphaerae DSM 17399T (96.1–96.4 %). This affiliation was also supported by rpoB-based phylogenetic analyses. Growth was observed at 20–40 °C (optimum, 30–37 °C) and at pH 5.0–9.0 (optimum, pH 6.0–7.0). The cells contained MK-7 as the sole respiratory quinone and anteiso-C15 : 0 as the major cellular fatty acid. Their cellular polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and 12 unidentified polar lipids. The diamino acid of their cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA–DNA hybridization value between THMBG22T and R24 was 84 %, and DNA–DNA relatedness to the most closely related species with a validly published name ( P. sacheonensis ) was 35–37 %. These results supported the assignment of the new isolates to the genus Paenibacillus and also distinguished them from the previously described species of the genus Paenibacillus . Hence, it is proposed that strains THMBG22T and R24 represent a novel species of the genus Paenibacillus , with the name Paenibacillus taihuensis sp. nov. The type strain is THMBG22T ( = CGMCC 1.10966T = NBRC 108766T).

Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes

The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.

Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum

Bacterial strain THMBM1(T) was isolated from decomposing algal scum that was collected during an algal bloom in Lake Taihu, Wuxi City, Jiangsu Province, China. Cells of strain THMBM1(T) were Gram-negative, facultatively anaerobic, non-motile rods. Colonies on tryptic soy agar were translucent and shiny with entire edges; yellow flexirubin-type pigments were produced. Growth was observed at 15-45 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 8.0) and in the presence of 0-4.0 % (w/v) NaCl (optimum 0-1.0 %). Strain THMBM1(T) contained MK-6 as the sole respiratory quinone and sym-homospermidine as the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 (53.2 %), iso-C17 : 0 3-OH (15.6 %) and iso-C17 : 1ω9c (11.9 %). The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The DNA G+C content was 36.8 mol% (Tm). Strain THMBM1(T) was closely related to members of the genus Chryseobacterium, with 16S rRNA gene sequence similarities ranging from 92.9 to 97.2 %, the highest sequence similarities being with Chryseobacterium taiwanense BCRC 17412(T) (97.2 %) and C. gambrini 5-1St1a(T) (97.1 %). DNA-DNA relatedness between strain THMBM1(T) and C. taiwanense JCM 21767(T) and C. gambrini DSM 18014(T) was 34.1  and 23.0 %, respectively. Based on these results, it is concluded that strain THMBM1(T) represents a novel species, for which the name Chryseobacterium taihuense sp. nov. is proposed. The type strain is THMBM1(T) ( = CGMCC 1.10941(T)  = NBRC 108747(T)). Emended descriptions of the genus Chryseobacterium and C. taiwanense, C. jejuense and C. indoltheticum are also proposed.