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Bute TF, Wyness A, Wasserman RJ, Dondofema F, Keates C, Dalu T. Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173059. [PMID: 38723976 DOI: 10.1016/j.scitotenv.2024.173059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g-1; Protein mean 65 μg g-1) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g-1; Protein mean 26 μg g-1). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.
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Affiliation(s)
- Tafara F Bute
- Department of Zoology and Entomology, Rhodes University, Makhanda 6140, South Africa.
| | - Adam Wyness
- Department of Zoology and Entomology, Rhodes University, Makhanda 6140, South Africa; Scottish Association for Marine Science, Oban PA37 1QA, United Kingdom
| | - Ryan J Wasserman
- Department of Zoology and Entomology, Rhodes University, Makhanda 6140, South Africa; South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
| | - Farai Dondofema
- Department of Geography and Environmental Sciences, University of Venda, Thohoyandou 0950, South Africa
| | - Chad Keates
- Department of Zoology and Entomology, Rhodes University, Makhanda 6140, South Africa; South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa
| | - Tatenda Dalu
- South African Institute for Aquatic Biodiversity, Makhanda 6140, South Africa; School of Biology and Environmental Sciences, University of Mpumalanga, Nelspruit 1200, South Africa
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Mugge RL, Moseley RD, Hamdan LJ. Substrate Specificity of Biofilms Proximate to Historic Shipwrecks. Microorganisms 2023; 11:2416. [PMID: 37894074 PMCID: PMC10608953 DOI: 10.3390/microorganisms11102416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.
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Affiliation(s)
- Rachel L. Mugge
- U.S. Naval Research Laboratory, Ocean Sciences Division, Stennis Space Center, MS 39529, USA;
| | - Rachel D. Moseley
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS 39564, USA
| | - Leila J. Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS 39564, USA
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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4
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Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms. Microbiol Res 2022; 265:127207. [DOI: 10.1016/j.micres.2022.127207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/17/2022] [Accepted: 09/18/2022] [Indexed: 11/21/2022]
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Liu JX, Zhu KC, Guo HY, Liu BS, Zhang N, Zhang DC. Effects of cysteine addition to low-fishmeal diets on the growth, anti-oxidative stress, intestine immunity, and Streptococcus agalactiae resistance in juvenile golden pompano (Trachinotus ovatus). Front Immunol 2022; 13:1066936. [DOI: 10.3389/fimmu.2022.1066936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
As the precursor of taurine, cysteine serves physiological functions, such as anti-oxidative stress and immune improvement. Investigation of cysteine and its derivatives has made positive progress in avian and mammalian species, yet the study and application of cysteine in aquatic animals are relatively rare. Therefore, we evaluated the effects of supplementing a low-fishmeal diet with various levels of cysteine on the growth, antioxidant capacity, intestine immunity, and resistance against Streptococcus agalactiae of the juvenile golden pompano (Trachinotus ovatus). According to our study, exogenous supplementation with 0.6-1.2% cysteine greatly increased the final body weight (FBW) and specific growth rate (SGR) of golden pompano compared to the control group. Under the present conditions, the optimum dietary cysteine supplementation level for golden pompano was 0.91% based on the polynomial regression analysis of SGR. Meanwhile, we found that the Nrf2/Keap1/HO-1 signaling pathway was notably upregulated with the increase of exogenous cysteine, which increased antioxidant enzyme activity in serum and gene expression in the intestine and reduced the level of reactive oxygen species (ROS) in the serum of golden pompano. In addition, morphological analysis of the midgut demonstrated that exogenous cysteine improved muscle thickness and villi length, which suggested that the physical barrier of the intestine was greatly strengthened by cysteine. Moreover, cysteine increased the diversity and relative abundance of the intestinal flora of golden pompano. Cysteine suppressed intestinal NF-κB/IKK/IκB signaling and pro-inflammatory cytokine mRNA levels. Conversely, intestinal anti-inflammatory cytokine gene expression and serum immune parameters were upregulated with the supplementary volume of cysteine and improved intestine immunity. Further, exogenous cysteine supplementation greatly reduced the mortality rate of golden pompano challenged with S. agalactiae. In general, our findings provide more valuable information and new insights into the rational use of cysteine in the culture of healthy aquatic animals.
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Effects of Selenium in Different Valences on the Community Structure and Microbial Functions of Biofilms. WATER 2022. [DOI: 10.3390/w14152394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
With the wide application of selenium (Se) in industrial production, different Se-based compounds (selenate and selenite) are produced and released into aquatic environments. The potential impacts of such Se compounds on the biofilms (a complex microbial aggregate in aquatic systems) need to be substantially explored. Herein, we investigated the responses of bacterial community diversity, composition and structure, and function of biofilms after 21 days of exposure to low concentrations (100 µg/L) and high concentrations (1 mg/L) of sodium selenate and sodium selenite, respectively. Distinct effects of selenium in different valences on the community structure and microbial functions of biofilms were observed. Compared with the controls, the addition of selenate and selenite solutions altered the richness of biofilms but not the diversity, which is dependent on the concentration and valences, with sodium selenite (1 mg/L) exhibiting a strong inhibition effect on community richness. Significant changes of community composition and structure were observed, with a significant increase in Proteobacteria (31.08–58.00%) and a significant decrease in Bacteroidetes (32.15–11.45%) after exposure to sodium selenite with high concentration. Also, different responses of gamma-Proteobacteria and alpha-Proteobacteria were observed between the sodium selenite and sodium selenate treatments. Moreover, results showed that sodium selenite could strengthen the function of the metabolism of biofilms, and the higher the concentration is, the more apparent the enhancement effect is. All these results suggested that the effects of different valence states of selenium were obvious, and sodium selenite with high concentration strongly changed the diversity, structure and function of biofilms.
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7
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Garrison CE, Roozbehi S, Mitra S, Corbett DR, Field EK. Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina. Front Microbiol 2022; 13:816573. [PMID: 35756005 PMCID: PMC9218724 DOI: 10.3389/fmicb.2022.816573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Hurricane frequencies and intensities are expected to increase under warming climate scenarios, increasing potential to disrupt microbial communities from steady-state conditions and alter ecosystem function. This study shows the impact of hurricane season on microbial community dynamics within the barrier island system of Outer Banks, North Carolina. We found that the passage of two sequential energetic hurricanes in 2018 (Florence and Michael) were correlated with shifts in total and active (DNA and RNA) portions of bacterial communities but not in archaeal communities, and within surface waters but not within the sediment. These microbial community shifts were distinct from non-hurricane season conditions, suggesting significant implications for nutrient cycling in nearshore and offshore environments. Hurricane-influenced marine sites in the coastal North Atlantic region had lower microbial community evenness and Shannon diversity, in addition to increased relative abundance of copiotrophic microbes compared to non-hurricane conditions. The abundance of functional genes associated with carbon and nitrogen cycling pathways were also correlated with the storm season, potentially shifting microbial communities at offshore sites from autotroph-dominated to heterotroph-dominated and leading to impacts on local carbon budgets. Understanding the geographic- and system-dependent responses of coastal microbial communities to extreme storm disturbances is critical for predicting impacts to nutrient cycling and ecosystem stability in current and future climate scenarios.
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Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Sara Roozbehi
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Siddhartha Mitra
- Department of Geological Sciences, East Carolina University, Greenville, NC, United States.,Integrated Coastal Programs, East Carolina University, Greenville, NC, United States
| | - D Reide Corbett
- Integrated Coastal Programs, East Carolina University, Greenville, NC, United States
| | - Erin K Field
- Department of Biology, East Carolina University, Greenville, NC, United States
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Du S, Sun X, Zhang J, Lin D, Chen R, Cui Y, Xiang S, Wu Z, Ding T. Metagenome-Assembled Genomes Reveal Mechanisms of Carbohydrate and Nitrogen Metabolism of Schistosomiasis-Transmitting Vector Biomphalaria Glabrata. Microbiol Spectr 2022; 10:e0184321. [PMID: 35254167 PMCID: PMC9045156 DOI: 10.1128/spectrum.01843-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
Biomphalaria glabrata transmits schistosomiasis mansoni which poses considerable risks to hundreds of thousands of people worldwide, and is widely used as a model organism for studies on the snail-schistosome relationship. Gut microbiota plays important roles in multiple aspects of host including development, metabolism, immunity, and even behavior; however, detailed information on the complete diversity and functional profiles of B. glabrata gut microbiota is still limited. This study is the first to reveal the gut microbiome of B. glabrata based on metagenome-assembled genome (MAG). A total of 28 gut samples spanning diet and age were sequenced and 84 individual microbial genomes with ≥ 70% completeness and ≤ 5% contamination were constructed. Bacteroidota and Proteobacteria were the dominant bacteria in the freshwater snail, unlike terrestrial organisms harboring many species of Firmicutes and Bacteroidota. The microbial consortia in B. glabrata helped in the digestion of complex polysaccharide such as starch, hemicellulose, and chitin for energy supply, and protected the snail from food poisoning and nitrate toxicity. Both microbial community and metabolism of B. glabrata were significantly altered by diet. The polysaccharide-degrading bacterium Chryseobacterium was enriched in the gut of snails fed with high-digestibility protein and high polysaccharide diet (HPHP). Notably, B. glabrata as a mobile repository can escalate biosafety issues regarding transmission of various pathogens such as Acinetobacter nosocomialis and Vibrio parahaemolyticus as well as multiple antibiotic resistance genes in the environment and to other organisms. IMPORTANCE The spread of aquatic gastropod Biomphalaria glabrata, an intermediate host of Schistosoma mansoni, exacerbates the burden of schistosomiasis disease worldwide. This study provides insights into the importance of microbiome for basic biological activities of freshwater snails, and offers a valuable microbial genome resource to fill the gap in the analysis of the snail-microbiota-parasite relationship. The results of this study clarified the reasons for the high adaptability of B. glabrata to diverse environments, and further illustrated the role of B. glabrata in accumulation of antibiotic resistance in the environment and spread of various pathogens. These findings have important implications for further exploration of the control of snail dissemination and schistosomiasis from a microbial perspective.
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Affiliation(s)
- Shuling Du
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xi Sun
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Jingxiang Zhang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Datao Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Runzhi Chen
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ying Cui
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Suoyu Xiang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhongdao Wu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Tao Ding
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
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Can Aggregate-Associated Organisms Influence the Fouling in a SWRO Desalination Plant? Microorganisms 2022; 10:microorganisms10040682. [PMID: 35456734 PMCID: PMC9032733 DOI: 10.3390/microorganisms10040682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/10/2022] Open
Abstract
This pilot study investigates the formation of aggregates within a desalination plant, before and after pre-treatment, as well as their potential impact on fouling. The objective is to provide an understanding of the biofouling potential of the feed water within a seawater reverse osmosis (SWRO) desalination plant, due to the limited removal of fouling precursors. The 16S and 18S rRNA was extracted from the water samples, and the aggregates and sequenced. Pre-treatment systems, within the plant remove < 5 µm precursors and organisms; however, smaller size particles progress through the plant, allowing for the formation of aggregates. These become hot spots for microbes, due to their nutrient gradients, facilitating the formation of niche environments, supporting the proliferation of those organisms. Aggregate-associated organisms are consistent with those identified on fouled SWRO membranes. This study examines, for the first time, the factors supporting the formation of aggregates within a desalination system, as well as their microbial communities and biofouling potential.
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Jiang Q, Jing H, Jiang Q, Zhang Y. Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps. MARINE POLLUTION BULLETIN 2022; 176:113458. [PMID: 35217425 DOI: 10.1016/j.marpolbul.2022.113458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 02/10/2022] [Indexed: 05/10/2023]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.
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Affiliation(s)
- QiuYun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China.
| | - QiuLong Jiang
- The College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai 201400, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Zhou G, Tao HB, Wen X, Wang YS, Peng H, Liu HZ, Yang XJ, Huang XM, Shi QS, Xie XB. Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals. CHEMOSPHERE 2022; 291:132766. [PMID: 34740703 DOI: 10.1016/j.chemosphere.2021.132766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/26/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.
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Affiliation(s)
- Gang Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hong-Bing Tao
- Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xia Wen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Ying-Si Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hong Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Hui-Zhong Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiu-Jiang Yang
- Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiao-Mo Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China; Guangdong Dimei Biotechnology Co., Ltd, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Qing-Shan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
| | - Xiao-Bao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510070, People's Republic of China.
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12
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Eckroat TJ, Greguske C, Hunnicutt DW. The Type 9 Secretion System Is Required for Flavobacterium johnsoniae Biofilm Formation. Front Microbiol 2021; 12:660887. [PMID: 34539591 PMCID: PMC8444969 DOI: 10.3389/fmicb.2021.660887] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Flavobacterium johnsoniae forms biofilms in low nutrient conditions. Protein secretion and cell motility may have roles in biofilm formation. The F. johnsoniae type IX secretion system (T9SS) is important for both secretion and motility. To determine the roles of each process in biofilm formation, mutants defective in secretion, in motility, or in both processes were tested for their effects on biofilm production using a crystal violet microplate assay. All mutants that lacked both motility and T9SS-mediated secretion failed to produce biofilms. A porV deletion mutant, which was severely defective for secretion, but was competent for motility, also produced negligible biofilm. In contrast, mutants that retained secretion but had defects in gliding formed biofilms. An sprB mutant that is severely but incompletely defective in gliding motility but retains a fully functional T9SS was similar to the wild type in biofilm formation. Mutants with truncations of the gldJ gene that compromise motility but not secretion showed partial reduction in biofilm formation compared to wild type. Unlike the sprB mutant, these gldJ truncation mutants were essentially nonmotile. The results show that a functional T9SS is required for biofilm formation. Gliding motility, while not required for biofilm formation, also appears to contribute to formation of a robust biofilm.
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Affiliation(s)
- Todd J. Eckroat
- School of Science, Penn State Erie, The Behrend College, Erie, PA, United States
| | - Camillus Greguske
- Division of Natural Science, St. Norbert College, De Pere, WI, United States
| | - David W. Hunnicutt
- Division of Natural Science, St. Norbert College, De Pere, WI, United States
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13
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Campana S, Busch K, Hentschel U, Muyzer G, de Goeij JM. DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM). Environ Microbiol 2021; 23:4489-4504. [PMID: 34159693 PMCID: PMC8453545 DOI: 10.1111/1462-2920.15642] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022]
Abstract
Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12 C) and labelled (13 C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.
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Affiliation(s)
- Sara Campana
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Kathrin Busch
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Ute Hentschel
- Department of Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Gerard Muyzer
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands
| | - Jasper M de Goeij
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, Netherlands.,CARMABI Foundation, Piscaderabaai z/n, P.O. Box 2090, Willemstad, Curaçao
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14
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Wilson JM, Chamberlain EJ, Erazo N, Carter ML, Bowman JS. Recurrent microbial community types driven by nearshore and seasonal processes in coastal Southern California. Environ Microbiol 2021; 23:3225-3239. [PMID: 33928761 DOI: 10.1111/1462-2920.15548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/26/2021] [Indexed: 01/04/2023]
Abstract
A multitude of concurrent biological and physical processes contribute to microbial community turnover, especially in highly dynamic coastal environments. Characterizing what factors contribute most to shifts in microbial community structure and the specific organisms that correlate with changes in the products of photosynthesis improves our understanding of nearshore microbial ecosystem functions. We conducted high frequency sampling in nearshore Southern California in order to capture sub-weekly microbial community dynamics. Microbial communities were characterized by flow cytometry and 16S rRNA gene sequencing, and placed in the context of physicochemical parameters. Within our time-series, season and nutrient availability corresponded to changes in dominant microbial community members. Concurrent aseasonal drivers with overlapping scales of variability were also apparent when we used network analysis to assess the microbial community as subsets of the whole. Our analyses revealed the microbial community as a mosaic, with overlapping groups of taxa that varied on different timescales and correlated with unique abiotic and biotic factors. Specifically, a subnetwork associated with chlorophyll a exhibited rapid turnover, indicating that ecologically important subsets of the microbial community can change on timescales different than and in response to factors other than those that govern turnover of most members of the assemblage.
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Affiliation(s)
- Jesse M Wilson
- Scripps Institution of Oceanography, UCSD, La Jolla, CA, USA
| | | | - Natalia Erazo
- Scripps Institution of Oceanography, UCSD, La Jolla, CA, USA
| | | | - Jeff S Bowman
- Scripps Institution of Oceanography, UCSD, La Jolla, CA, USA.,Center for Microbiome Innovation, UCSD, La Jolla, CA, USA.,Center for Marine Biodiversity and Conservation, UCSD, La Jolla, CA, USA
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15
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Garrison CE, Field EK. Introducing a "core steel microbiome" and community functional analysis associated with microbially influenced corrosion. FEMS Microbiol Ecol 2021; 97:5998222. [PMID: 33220682 DOI: 10.1093/femsec/fiaa237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms attached to aquatic steel structures play key roles in nutrient cycling and structural degradation processes. Corrosion-causing microbes are often the focus of studies involving microbially influenced corrosion, yet the roles of remaining community members remain unclear. This study characterizes the composition and functional potential of a 'core steel microbiome' across stainless steel types (304 and 316) and historic shipwreck steel along salinity gradients in North Carolina estuaries. We found higher phylogenetic evenness and diversity on steel surfaces compared to sediment, and at lower salinities. The core steel microbiome was composed of heterotrophic generalist taxa, and community composition was most strongly influenced by salinity. Substrate type was a secondary factor becoming more influential at higher salinities. The core steel microbiome included members of Sphingobacteriia, Cytophagia, Anaerolineaceae, Verrucomicrobiaceae, Chitinophagaceae, and Rheinheimera. While salinity differences led to phylogenetic separations across microbial community assemblages, functional genes were conserved across salinity and steel type. Generalist taxa on steel surfaces likely provide functional stability and biofilm protection for the community with limited functional trade-offs compared to surrounding environments. Further, characterization of a core steel microbiome increases the understanding of these complex steel surface microbial communities and their similarities to core microbiomes in other environments.
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Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| | - Erin K Field
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
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16
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Eswaran R, Khandeparker L. Influence of salinity stress on bacterial community composition and β-glucosidase activity in a tropical estuary: Elucidation through microcosm experiments. MARINE ENVIRONMENTAL RESEARCH 2020; 159:104997. [PMID: 32662433 DOI: 10.1016/j.marenvres.2020.104997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
The influence of changing salinity on community composition and functional activity (Bacterial Production (BP) and ectoenzyme activity) of major bacterial taxa was evaluated using microcosm experiments in a tropical monsoon influenced estuary. Natural bacterial inocula at different salinities, representing marine, brackish, and freshwater, were inter-transferred and elucidated their response with an emphasis on community composition and β-Glucosidase (BGase) activity. The results revealed a significant decrease in the total bacterial count (TBC) and BP on the translocation of bacterial inocula to different salinity conditions in the case of freshwater bacteria. However, a significant increase in BGase activity coupled with shifts in the studied bacterial groups was evident in the case of marine as well as freshwater bacteria. Quantitative PCR (qPCR) revealed a shift in major bacterial taxa upon translocation to different waters, which was dependent on salinity and the source of inocula. Redundancy and qPCR analyses showed that members belonging to Gammaproteobacteria and Betaproteobacteria were higher, and possibly influenced BGase activity in marine and freshwater, respectively. Translocation of marine inocula to brackish and freshwater resulted in an emergence of Bacteroidetes, Actinobacteria, and Betaproteobacteria, respectively. Whereas, when freshwater inocula were translocated to marine or brackish water, Alphaproteobacteria and Gammaproteobacteria taxa emerged, and this was coupled with increased BGase activity. In contrast, brackish water bacteria showed a strong persistence in bacterial community composition when translocated to different salinities within this estuary. Such phylogenetic persistence or changes suggests species level shifts in specific bacterial taxa, and unravelling the same using different functional gene markers would ascertain their role in organic matter processing and is way forward.
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Affiliation(s)
- Ranjith Eswaran
- CSIR - National Institute of Oceanography, Dona Paula, Goa, India; School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao, Goa, India
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17
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Microbiologically influenced corrosion of marine steels within the interaction between steel and biofilms: a brief view. Appl Microbiol Biotechnol 2019; 104:515-525. [PMID: 31807887 DOI: 10.1007/s00253-019-10184-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 10/25/2022]
Abstract
Marine is the harshest corrosive environment where almost all marine underwater equipment and facilities undergo corrosion caused by marine microorganisms. With the development of marine resources globally, the marine engineering and relevant infrastructures have increased exponentially. Microbiologically influenced corrosion (MIC) leads to severe safety accidents and great economic losses. The specific aggregation of corrosive microbial communities and their interactions with materials conform to a typical ecological adaptation mechanism. On the one hand, corrosive biofilms in the marine environment selectively colonize on a specific steel substrate by utilizing their complex community composition and various extracellular polymeric substances; on the other hand, the elemental composition and surface microstructure of different engineering steels affect the microbial community and corrosive process. MIC in the marine environment is a dynamic process evolving with the formation of corrosive biofilms and corrosion products. In this mini-review, the interactions between corrosive biofilm and steel substrates are explored and discussed, especially those conducted in situ in the marine environment. Herein, the important role of iron in the dynamic process of marine corrosion is highlighted.
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18
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Munar MP, Takahashi H, Okamura Y. Discovery of a Novel Gene Conferring Tellurite Tolerance Through Tellurite Reduction to Escherichia coli Transformant in Marine Sediment Metagenomic Library. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:762-772. [PMID: 31637558 DOI: 10.1007/s10126-019-09922-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Metagenomic library construction using a marine sediment-enrichment was employed in order to recover tellurium from tellurite, a tellurium oxyanion, dissolved in water and then functional screening was performed to discover a novel gene related to tellurite reduction. Transmission electron microscopy (TEM) revealed the formation of intracellular Te crystals in Escherichia coli cells transformed with a specific DNA fragment from the marine sediment metagenome. The metagenome fragment was composed of 691 bp and showed low homology to known proteins. Phylogenetic analysis suggested that the metagenome fragment was related to Pseudomonas stutzeri. Cloning and expression of an open reading frame (ORF) on the metagenome fragment validated the role of the fragment in conferring tellurite resistance and tellurite-reducing activity to E. coli host cells. E. coli transformant containing the ORF1 showed resistance to 1 mM Na2TeO3. The optimal tellurite-reducing activity of cells containing the ORF1 was recorded at 37 °C and pH 7.0.
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Affiliation(s)
- Madison Pascual Munar
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan
| | - Hirokazu Takahashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yoshiko Okamura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Hiroshima, Japan.
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan.
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19
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Su X, Xue B, Wang Y, Hashmi MZ, Lin H, Chen J, Mei R, Wang Z, Sun F. Bacterial community shifts evaluation in the sediments of Puyang River and its nitrogen removal capabilities exploration by resuscitation promoting factor. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 179:188-197. [PMID: 31048215 DOI: 10.1016/j.ecoenv.2019.04.067] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 06/09/2023]
Abstract
Identifying indigenous bacterial community and exploring the potential of native microorganisms are crucial for in situ bioremediation of nitrogenous pollutants in water bodies. This study evaluated the bacterial communities of sediment samples from a nitrogen polluted river, and revealed the possible environmental factors shaping the bacterial populations. Importantly, viable but non-culturable bacteria which possessed nitrogen removal capabilities in indigenous population of the sediments were explored by resuscitation promoting factor (Rpf). It was found that the sediments from upstream (URS) and lower stream (LRS) of Puyang river showed both different pollutants levels and bacterial community. Nitrate nitrogen, organic carbon and ammonium nitrogen probably had a significant effect on bacterial compositions between URS and LRS. From URS and LRS, a total of thirteen strains with heterotrophic nitrification ability were resuscitated by Rpf addition, which belonged to genera Bacillus, Pseudomonas, Stenotrophomonas and Acinetobacter. Among them, the strain Pseudomonas sp. SSPR1 was found to display high removal capabilities of simultaneous nitrification and denitrification, and the average ammonium and nitrate removal rates were 2.23 and 0.86 mg/(L·h), respectively. These resuscitated strains could be considered to be used for biological nitrogen removal in rivers and their receiving water bodies.
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Affiliation(s)
- Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Binbing Xue
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Yuyang Wang
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | | | - Hongjun Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Jianrong Chen
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Rongwu Mei
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | - Zhen Wang
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, 310007, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China.
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20
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Muthukrishnan T, Al Khaburi M, Abed RMM. Fouling Microbial Communities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific? MICROBIAL ECOLOGY 2019; 78:361-374. [PMID: 30535914 DOI: 10.1007/s00248-018-1303-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 11/27/2018] [Indexed: 05/20/2023]
Abstract
Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial communities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable operational taxonomic unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial communities based on substrate (analysis of similarity (ANOSIM), R = 0.45-0.97, p < 0.03) and location (ANOSIM, R = 0.56, p < 0.0001). The bacterial genera Microcystis and Hydrogenophaga and the diatoms Licmophora and Mastogloia were specifically detected on plastics. Desulfovibrio and Pseudomonas spp. exhibited their highest abundance on steel and Corynebacterium spp. on wood. Scanning electron microscopy (SEM) revealed fissure formation on PET and PE, indicating physical degradation. The presence of free radicals on PET and carbonyl bonds (C=O) on PE, as revealed by Fourier transform infrared (FTIR) spectroscopy, indicated abiotic degradation while hydroxyl groups and spectral peaks for proteins and polysaccharides on PE indicated biotic degradation. We conclude that fouling microbial communities are not only substrate-specific but also location-specific and microbes developing on plastics could potentially contribute to their degradation in the marine environment.
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Affiliation(s)
- Thirumahal Muthukrishnan
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman
| | - Maryam Al Khaburi
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman
| | - Raeid M M Abed
- Biology Department, College of Science, Sultan Qaboos University, P. O. Box 36, PC, 123, Al Khoud, Sultanate of Oman.
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21
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Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. ISME JOURNAL 2019; 13:2817-2833. [PMID: 31320727 PMCID: PMC6794264 DOI: 10.1038/s41396-019-0472-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 06/11/2019] [Accepted: 06/15/2019] [Indexed: 01/06/2023]
Abstract
Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.
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22
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Zhao C, Long J, Liao H, Zheng C, Li J, Liu L, Zhang M. Dynamics of soil microbial communities following vegetation succession in a karst mountain ecosystem, Southwest China. Sci Rep 2019; 9:2160. [PMID: 30770852 PMCID: PMC6377603 DOI: 10.1038/s41598-018-36886-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 11/22/2018] [Indexed: 11/09/2022] Open
Abstract
The interaction between soil property and soil microbial community in karst area still remains an open question. The characteristics of soil physicochemical properties and microbial community structure and their relationship under five vegetation succession stages (grassland, shrub land, secondary forest, plantation forest, and natural forest) at two soil depths (0–10 cm and 10–20 cm) were explored in a karst mountain ecosystem. We found that soil moisture content (SMC) and pH increased with soil depth across vegetation succession. The highest content of soil nutrients was found in the natural forest stage at both soil depths. The total PLFAs, the abundance of Gram-positive (GP) bacteria, actinomycetes (ACT), fungi, and arbuscular mycorrhizal fungi (AMF) were significantly (P < 0.05) related to variations with soil total carbon (TC) and total nitrogen (TN). Furthermore, the distribution of soil microbial community distinctly differed in vegetation succession both at two soil layers which was demonstrated by Principal-coordinates analysis. Redundancy analyses patterns indicated that soil TC and TN were positively related to cy19:0 and 10Me 16:0, but an opposite relationship with a15:0. Changes of soil microbial communities were significantly determined by vegetation succession, and soil microbial community structure can be a sensitive indicator to reflect the stabilization of karst mountain ecosystem, southwest of China.
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Affiliation(s)
- Chang Zhao
- Guizhou Key Laboratory of Mountain Environment, Guizhou Normal University, Guiyang, 550001, China
| | - Jian Long
- Guizhou Key Laboratory of Mountain Environment, Guizhou Normal University, Guiyang, 550001, China.
| | - Hongkai Liao
- Guizhou Key Laboratory of Mountain Environment, Guizhou Normal University, Guiyang, 550001, China
| | - Chunli Zheng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Li
- Department of Geography and Environmental Science, Guizhou Normal University, Guiyang, 550001, China
| | - Lingfei Liu
- Guizhou Key Laboratory of Mountain Environment, Guizhou Normal University, Guiyang, 550001, China
| | - Mingjiang Zhang
- Guizhou Key Laboratory of Mountain Environment, Guizhou Normal University, Guiyang, 550001, China
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23
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Cui H, Su X, Chen F, Holland M, Yang S, Liang J, Su P, Dong H, Hou W. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. MARINE ENVIRONMENTAL RESEARCH 2019; 144:230-239. [PMID: 30732863 DOI: 10.1016/j.marenvres.2019.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/29/2018] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
Cold seep is a unique habitat for microorganisms in deep marine sediments, and microbial communities and biogeochemical processes are still poorly understood, especially in relation to hydrate-bearing geo-systems. In this study, two cold seep systems were sampled and microbial diversity was studied at Site GMGS2-08 in the northern part of the South China Sea (SCS) during the GMGS2 gas hydrate expedition. The current cold seep system was composed of a sulfate methane transition zone (SMTZ) and an upper gas hydrate zone (UGHZ). The buried cold seep system was composed of an authigenic carbonate zone (ACZ) and a lower gas hydrate zone (LGHZ). These drill core samples provided an excellent opportunity for analyzing the microbial abundance and diversity based on quantitative polymerase chain reaction (qPCR) and high-throughput 16S rRNA gene sequencing. Compared to previous studies, the high relative abundance of ANME-1b, a clade of anaerobic methanotrophic archaea (ANME), may perform anaerobic oxidation of methane (AOM) in collaboration with ANME-2c and Desulfobacteraceae in the SMTZ, and the high relative abundances of Hadesarchaea, ANME-1b archaea and Aerophobetes bacteria were found in the gas hydrate zone (GHZ) at Site GMGS2-08. ANME-1b, detected in the GHZ, might mainly mediate the AOM process, and the process might occur in a wide depth range within the LGHZ. Moreover, bacterial communities were significantly different between the GHZ and non-GHZ sediments. In the ACZ, archaeal communities were different between the two samples from the upper and the lower layers, while bacterial communities shared similarities. Overall, this new record of cold seep microbial diversity at Site GMGS2-08 showed the complexity of the interaction between biogeochemical reactions and environmental conditions.
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Affiliation(s)
- Hongpeng Cui
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Xin Su
- School of Ocean Sciences, China University of Geosciences, Beijing, 100083, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.
| | - Fang Chen
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | | | - Shengxiong Yang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Jinqiang Liang
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China.
| | - Pibo Su
- Guangzhou Marine Geological Survey, Guangzhou, 510075, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Department of Geology and Environmental Earth Science, Miami University, OH, 45056, USA
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
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24
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Lin JD, Lemay MA, Parfrey LW. Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera. Front Microbiol 2018; 9:1914. [PMID: 30177919 PMCID: PMC6110156 DOI: 10.3389/fmicb.2018.01914] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bacteria are integral to marine carbon cycling. They transfer organic carbon to higher trophic levels and remineralise it into inorganic forms. Kelp forests are among the most productive ecosystems within the global oceans, yet the diversity and metabolic capacity of bacteria that transform kelp carbon is poorly understood. Here, we use 16S amplicon and metagenomic shotgun sequencing to survey bacterial communities associated with the surfaces of the giant kelp Macrocystis pyrifera and assess the capacity of these bacteria for carbohydrate metabolism. We find that Macrocystis-associated communities are distinct from the water column, and that they become more diverse and shift in composition with blade depth, which is a proxy for tissue age. These patterns are also observed in metagenomic functional profiles, though the broader functional groups—carbohydrate active enzyme families—are largely consistent across samples and depths. Additionally, we assayed more than 250 isolates cultured from Macrocystis blades and the surrounding water column for the ability to utilize alginate, the primary polysaccharide in Macrocystis tissue. The majority of cultured bacteria (66%) demonstrated this capacity; we find that alginate utilization is patchily distributed across diverse genera in the Bacteroidetes and Proteobacteria, yet can also vary between isolates with identical 16S rRNA sequences. The genes encoding enzymes involved in alginate metabolism were detected in metagenomic data across taxonomically diverse bacterial communities, further indicating this capacity is likely widespread amongst bacteria in kelp forests. Overall, the M. pyrifera epibiota shifts across a depth gradient, demonstrating a connection between bacterial assemblage and host tissue state.
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Affiliation(s)
- Jordan D Lin
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada
| | - Matthew A Lemay
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Laura W Parfrey
- Department of Botany, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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Hede N, Khandeparker L. Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments. MICROBIAL ECOLOGY 2018; 76:314-327. [PMID: 29380028 DOI: 10.1007/s00248-018-1149-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Ballast tank biofilms pose an additional risk of microbial invasion if sloughed off during ballasting operations, yet their significance and invasion biology is poorly understood. In this study, biofilms developed in marine and freshwater locations were exposed to prolonged darkness and aging by mimicking ballast water conditions in the laboratory. Upon prolonged darkness, the decay of phytoplankton, as indicated by the decrease in chlorophyll a in marine biofilms, led to remineralization and enhanced bacterial and protist populations. However, the same trend was not observed in the case of freshwater biofilms wherein the microbial parameters (i.e., bacteria, protists) and chlorophyll a decreased drastically. The bacterial community structure in such conditions was evaluated by real-time quantitative PCR (qPCR), and results showed that the biofilm bacterial communities changed significantly over a period of time. α-Proteobacteria was the most stable taxonomic group in the marine biofilms under dark conditions. However, β-proteobacteria dominated the freshwater biofilms and seemed to play an important role in organic matter remineralization. γ-Proteobacteria, which includes most of the pathogenic genera, were affected significantly and decreased in both the types of biofilms. This study revealed that marine biofilm communities were able to adapt better to the dark conditions while freshwater biofilm communities collapsed. Adaptation of tolerant bacterial communities, regeneration of nutrients via cell lysis, and presence of grazers appeared to be key factors for survival upon prolonged darkness. However, the fate of biofilm communities upon discharge in the new environment and their invasion potential is an important topic for future investigation.
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Affiliation(s)
- Niyati Hede
- CSIR - National Institute of Oceanography, Dona Paula, Goa, 403 004, India
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Kegler HF, Hassenrück C, Kegler P, Jennerjahn TC, Lukman M, Jompa J, Gärdes A. Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities. PeerJ 2018; 6:e4555. [PMID: 29761035 PMCID: PMC5944435 DOI: 10.7717/peerj.4555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/09/2018] [Indexed: 12/30/2022] Open
Abstract
Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function.
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Affiliation(s)
- Hauke F. Kegler
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
- Faculty of Biology and Chemistry (FB2), University of Bremen, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Pia Kegler
- Department of Ecology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Tim C. Jennerjahn
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
| | - Muhammad Lukman
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Jamaluddin Jompa
- Department of Marine Science, Universitas Hasanuddin, Makassar, Indonesia
| | - Astrid Gärdes
- Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Research, Bremen, Germany
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Anupama R, Mukherjee A, Babu S. Gene-centric metegenome analysis reveals diversity of Pseudomonas aeruginosa biofilm gene orthologs in fresh water ecosystem. Genomics 2018; 110:89-97. [DOI: 10.1016/j.ygeno.2017.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 01/22/2023]
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Briand JF, Barani A, Garnier C, Réhel K, Urvois F, LePoupon C, Bouchez A, Debroas D, Bressy C. Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments. MICROBIAL ECOLOGY 2017; 74:585-598. [PMID: 28374061 DOI: 10.1007/s00248-017-0966-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/14/2017] [Indexed: 06/07/2023]
Abstract
Surface colonization in seawater first corresponds to the selection of specific microbial biofilm communities. By coupling flow cytometry, microscopy and high throughput sequencing (HTS, 454 pyrosequencing) with artificial surfaces and environmental analyses, we intend to identify the contribution of biofilm community drivers at two contrasted French sites, one temperate and eutrophic (Lorient, Atlantic coast) and the other at a mesotrophic but highly contaminated bay (Toulon, North-Western Mediterranean Sea). Microbial communities were shaped by high temperatures, salinity and lead at Toulon by but nutrients and DOC at Lorient. Coatings including pyrithione exhibited a significant decrease of their microbial densities except for nanoeukaryotes. Clustering of communities was mainly based on the surface type and secondly the site, whereas seasons appeared of less importance. The in-depth HTS revealed that γ- and α-proteobacteria, but also Bacteroidetes, dominated highly diversified bacterial communities with a relative low β-diversity. Sensitivity to biocides released by the tested antifouling coatings could be noticed at different taxonomic levels: the percentage of Bacteroidetes overall decreased with the presence of pyrithione, whereas the α/γ-proteobacteria ratio decreased at Toulon when increased at Lorient. Small diatom cells (Amphora and Navicula spp.) dominated on all surfaces, whereas site-specific sub-dominant taxa appeared clearly more sensitive to biocides. This overall approach exhibited the critical significance of surface characteristics in biofilm community shaping.
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Affiliation(s)
| | - Aude Barani
- CNRS/INSU, IRD, Institut Méditerranéen d'Océanologie (MIO), Université d'Aix-Marseille, Université de Toulon, Marseille, France
| | | | - Karine Réhel
- LBCM -EA 3883, IUEM, Université de Bretagne Sud, Lorient, France
| | - Félix Urvois
- MAPIEM-EA 4323, Université de Toulon, La Garde, France
| | | | - Agnès Bouchez
- UMR CARRTEL, INRA, Université Savoie Mont Blanc, Thonon-Les-Bains, France
| | - Didier Debroas
- Laboratoire "Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, F-63000, Clermont-Ferrand, France
- UMR 6023, LMGE, CNRS, F-63171, Aubiere, France
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Tiwari R, Nain L, Labrou NE, Shukla P. Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 2017; 44:244-257. [DOI: 10.1080/1040841x.2017.1337713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rameshwar Tiwari
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Nikolaos E. Labrou
- Department of Biotechnology, School of Food, Biotechnology and Development, Laboratory of Enzyme Technology, Agricultural University of Athens, Athens, Greece
| | - Pratyoosh Shukla
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Kegler HF, Lukman M, Teichberg M, Plass-Johnson J, Hassenrück C, Wild C, Gärdes A. Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia. Front Microbiol 2017; 8:662. [PMID: 28473810 PMCID: PMC5397486 DOI: 10.3389/fmicb.2017.00662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/31/2017] [Indexed: 12/04/2022] Open
Abstract
Coastal eutrophication is a key driver of shifts in bacterial communities on coral reefs. With fringing and patch reefs at varying distances from the coast the Spermonde Archipelago in southern Sulawesi, Indonesia offers ideal conditions to study the effects of coastal eutrophication along a spatially defined gradient. The present study investigated bacterial community composition of three coral reef habitats: the water column, sediments, and mucus of the hard coral genus Fungia, along that cross-shelf environmental and water quality gradient. The main research questions were: (1) How do water quality and bacterial community composition change along a coastal shelf gradient? (2) Which water quality parameters influence bacterial community composition? (3) Is there a difference in bacterial community composition among the investigated habitats? For this purpose, a range of key water parameters were measured at eight stations in distances from 2 to 55 km from urban Makassar. This was supplemented by sampling of bacterial communities of important microbial habitats using 454 pyrosequencing. Findings revealed that the population center Makassar had a strong effect on the concentrations of Chlorophyll a, suspended particulate matter (SPM), and transparent exopolymer particles (TEP), which were all significantly elevated at the inshore compared the other seven sites. Shifts in the bacterial communities were specific to each sampled habitat. Two OTUs, belonging to the genera Escherichia/Shigella (Gammaproteobacteria) and Ralstonia (Betaproteobacteria), respectively, both dominated the bacterial community composition of the both size fractions of the water column and coral mucus. The sampled reef sediments were more diverse, and no single OTUs was dominant. There was no gradual shift in bacterial classes or OTUs within the sampled habitats. In addition, we observed very distinct communities between the investigated habitats. Our data show strong changes in the bacterial community composition at the inshore site for water column and sediment samples. Alarmingly, there was generally a high prevalence of potentially pathogenic bacteria across the entire gradient.
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Affiliation(s)
- Hauke F Kegler
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Muhammad Lukman
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin UniversitySouth Sulawesi, Indonesia
| | - Mirta Teichberg
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany
| | - Jeremiah Plass-Johnson
- Algae and Seagrass Ecology, Department of Ecology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,Centre for Ocean Life, National Institute of Aquatic Resources (DTU-Aqua), Technical University of DenmarkCharlottenlund, Denmark
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany.,HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Christian Wild
- Faculty of Biology and Chemistry (FB 2), University of BremenBremen, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz Center for Tropical Marine ResearchBremen, Germany
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31
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A glimpse of the diversity of complex polysaccharide-degrading culturable bacteria from Kongsfjorden, Arctic Ocean. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-016-1252-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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32
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Creating Economic Incentives for Waste Disposal in Developing Countries Using the MixAlco Process. Appl Biochem Biotechnol 2016; 181:294-308. [DOI: 10.1007/s12010-016-2213-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022]
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Geng H, Sale KL, Tran-Gyamfi MB, Lane TW, Yu ET. Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures. MICROBIAL ECOLOGY 2016; 72:14-24. [PMID: 26956183 DOI: 10.1007/s00248-016-0746-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.
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Affiliation(s)
- Haifeng Geng
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Kenneth L Sale
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Mary Bao Tran-Gyamfi
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Todd W Lane
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA.
| | - Eizadora T Yu
- Department of Systems Biology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
- Institute of Chemistry, National Science Complex, University of the Philippines, Diliman Quezon City, 1101, Philippines
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Wong MT, Wang W, Lacourt M, Couturier M, Edwards EA, Master ER. Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus). Front Microbiol 2016; 7:961. [PMID: 27446004 PMCID: PMC4914502 DOI: 10.3389/fmicb.2016.00961] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/03/2016] [Indexed: 02/01/2023] Open
Abstract
Strategic enrichment of microcosms derived from wood foragers can facilitate the discovery of key microbes that produce enzymes for the bioconversion of plant fiber (i.e., lignocellulose) into valuable chemicals and energy. In this study, lignocellulose-degrading microorganisms from the digestive systems of Canadian beaver (Castor canadensis) and North American moose (Alces americanus) were enriched under methanogenic conditions for over 3 years using various wood-derived substrates, including (i) cellulose (C), (ii) cellulose + lignosulphonate (CL), (iii) cellulose + tannic acid (CT), and (iv) poplar hydrolysate (PH). Substantial improvement in the conversion of amended organic substrates into biogas was observed in both beaver dropping and moose rumen enrichment cultures over the enrichment phases (up to 0.36–0.68 ml biogas/mg COD added), except for enrichments amended with tannic acid where conversion was approximately 0.15 ml biogas/mg COD added. Multiplex-pyrosequencing of 16S rRNA genes revealed systematic shifts in the population of Firmicutes, Bacteroidetes, Chlorobi, Spirochaetes, Chloroflexi, and Elusimicrobia in response to the enrichment. These shifts were predominantly substrate driven, not inoculum driven, as revealed by both UPGMA clustering pattern and OTU distribution. Additionally, the relative abundance of multiple OTUs from poorly defined taxonomic lineages increased from less than 1% to 25–50% in microcosms amended with lignocellulosic substrates, including OTUs from classes SJA-28, Endomicrobia, orders Bacteroidales, OPB54, and family Lachnospiraceae. This study provides the first direct comparison of shifts in microbial communities that occurred in different environmental samples in response to multiple relevant lignocellulosic carbon sources, and demonstrates the potential of enrichment to increase the abundance of key lignocellulolytic microorganisms and encoded activities.
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Affiliation(s)
- Mabel T Wong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Michael Lacourt
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Marie Couturier
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto ON, Canada
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Ventorino V, Parillo R, Testa A, Viscardi S, Espresso F, Pepe O. Chestnut green waste composting for sustainable forest management: Microbiota dynamics and impact on plant disease control. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2016; 166:168-77. [PMID: 26496847 DOI: 10.1016/j.jenvman.2015.10.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 09/25/2015] [Accepted: 10/11/2015] [Indexed: 05/03/2023]
Abstract
Making compost from chestnut lignocellulosic waste is a possible sustainable management strategy for forests that employs a high-quality renewable organic resource. Characterization of the microbiota involved in composting is essential to better understand the entire process as well as the properties of the final product. Therefore, this study investigated the microbial communities involved in the composting of chestnut residues obtained from tree cleaning and pruning. The culture-independent approach taken highlighted the fact that the microbiota varied only slightly during the process, with the exception of those of the starting substrate and mature compost. The statistical analysis indicated that most of the bacterial and fungal species in the chestnut compost persisted during composting. The dominant microbial population detected during the process belonged to genera known to degrade recalcitrant lignocellulosic materials. Specifically, we identified fungal genera, such as Penicillium, Fusarium, Cladosporium, Aspergillus and Mucor, and prokaryotic species affiliated with Bacilli, Actinobacteria, Flavobacteria and γ-Proteobacteria. The suppressive properties of compost supplements for the biocontrol of Sclerotinia minor and Rhizoctonia solani were also investigated. Compared to pure substrate, the addition of compost to the peat-based growth substrates resulted in a significant reduction of disease in tomato plants of up to 70 % or 51 % in the presence of Sclerotinia minor or Rhizoctonia solani, respectively. The obtained results were related to the presence of putative bio-control agents and plant growth-promoting rhizobacteria belonging to the genera Azotobacter, Pseudomonas, Stenotrophomonas, Bacillus, Flavobacterium, Streptomyces and Actinomyces in the chestnut compost. The composting of chestnut waste may represent a sustainable agricultural practice for disposing of lignocellulosic waste by transforming it into green waste compost that can be used to improve the fitness of agricultural plants.
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Affiliation(s)
- Valeria Ventorino
- Department of Agriculture, Division of Microbiology, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy
| | - Rita Parillo
- Department of Agriculture, Division of Biology and Protection of Agricultural and Forest Systems, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy
| | - Antonino Testa
- Department of Agriculture, Division of Biology and Protection of Agricultural and Forest Systems, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy
| | - Sharon Viscardi
- Department of Agriculture, Division of Microbiology, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy
| | - Francesco Espresso
- Department of Agriculture, Division of Microbiology, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy
| | - Olimpia Pepe
- Department of Agriculture, Division of Microbiology, University of Naples Federico II, Via Università, 100, 80055, Portici, NA, Italy.
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Lawes JC, Neilan BA, Brown MV, Clark GF, Johnston EL. Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms. BIOFOULING 2016; 32:57-69. [PMID: 26751559 DOI: 10.1080/08927014.2015.1126581] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Biofilms are integral to many marine processes but their formation and function may be affected by anthropogenic inputs that alter environmental conditions, including fertilisers that increase nutrients. Density composition and connectivity of biofilms developed in situ (under ambient and elevated nutrients) were compared using 454-pyrosequencing of the 16S gene. Elevated nutrients shifted community composition from bacteria involved in higher processes (eg Pseudoalteromonas spp. invertebrate recruitment) towards more nutrient-tolerant bacterial species (eg Terendinibacter sp.). This may enable the persistence of biofilm communities by increasing resistance to nutrient inputs. A core biofilm microbiome was identified (predominantly Alteromonadales and Oceanospirillales) and revealed shifts in abundances of core microbes that could indicate enrichment by fertilisers. Fertiliser decreased density and connectivity within biofilms indicating that associations were disrupted perhaps via changes to energetic allocations within the core microbiome. Density composition and connectivity changes suggest nutrients can affect the stability and function of these important marine communities.
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Affiliation(s)
- Jasmin C Lawes
- a School of Biological Earth and Environmental Sciences, University of New South Wales , Sydney , Australia
| | - Brett A Neilan
- b School of Biotechnology and Biomedical Sciences, University of New South Wales , Sydney , Australia
| | - Mark V Brown
- a School of Biological Earth and Environmental Sciences, University of New South Wales , Sydney , Australia
- b School of Biotechnology and Biomedical Sciences, University of New South Wales , Sydney , Australia
| | - Graeme F Clark
- a School of Biological Earth and Environmental Sciences, University of New South Wales , Sydney , Australia
| | - Emma L Johnston
- a School of Biological Earth and Environmental Sciences, University of New South Wales , Sydney , Australia
- c Sydney Institute of Marine Science , Sydney , Australia
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments. PLoS One 2015; 10:e0143917. [PMID: 26633175 PMCID: PMC4669084 DOI: 10.1371/journal.pone.0143917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/23/2022] Open
Abstract
More than 50% of terrestrially-derived organic carbon (terrOC) flux from the continents to the ocean is remineralised in the coastal zone despite its perceived high refractivity. The efficient degradation of terrOC in the marine environment could be fuelled by labile marine-derived material, a phenomenon known as “priming effect”, but experimental data to confirm this mechanism are lacking. We tested this hypothesis by treating coastal sediments with 13C-lignocellulose, as a proxy for terrOC, with and without addition of unlabelled diatom detritus that served as the priming inducer. The occurrence of priming was assessed by the difference in lignocellulose mineralisation between diatom-amended treatments and controls in aerobic sediment slurries. Priming of lignocellulose degradation was observed only at the initial stages of the experiment (day 7) and coincided with overall high microbial activity as exemplified by total CO2 production. Lignocellulose mineralisation did not differ consistently between diatom treatments and control for the remaining experimental time (days 14–28). Based on this pattern, we hypothesize that the faster initiation of lignocellulose mineralisation in diatom-amended treatments is attributed to the decomposition of accessible polysaccharide components within the lignocellulose complex by activated diatom degraders. The fact that diatom-degraders contributed to lignocellulose degradation was also supported by the different patterns in 13C-enrichment of phospholipid fatty acids between treatments. Although we did not observe differences between treatments in the total quantity of respired lignocellulose at the end of the experiment, differences in timing could be important in natural ecosystems where the amount of time that a certain compound is subject to aerobic degradation before burial to deeper anoxic sediments may be limited.
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Sanli K, Bengtsson-Palme J, Nilsson RH, Kristiansson E, Alm Rosenblad M, Blanck H, Eriksson KM. Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. Front Microbiol 2015; 6:1192. [PMID: 26579098 PMCID: PMC4626570 DOI: 10.3389/fmicb.2015.01192] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/13/2015] [Indexed: 11/13/2022] Open
Abstract
Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans, and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.
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Affiliation(s)
- Kemal Sanli
- Department of Biological and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology Gothenburg, Sweden
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg Gothenburg, Sweden
| | - Hans Blanck
- Department of Biological and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Karl M Eriksson
- Department of Shipping and Marine Technology, Chalmers University of Technology Gothenburg, Sweden
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Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, Brinkhoff T, Simon M. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol 2015; 17:3822-31. [DOI: 10.1111/1462-2920.12842] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Maren A. Seibt
- ICBM-MPI Bridging Group for Marine Geochemistry; Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory; Institute of Microbiology and Genetics; University of Göttingen; Göttingen 37077 Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg 26129 Germany
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Boutard M, Cerisy T, Nogue PY, Alberti A, Weissenbach J, Salanoubat M, Tolonen AC. Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass. PLoS Genet 2014; 10:e1004773. [PMID: 25393313 PMCID: PMC4230839 DOI: 10.1371/journal.pgen.1004773] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/24/2014] [Indexed: 12/16/2022] Open
Abstract
Microbial metabolism of plant polysaccharides is an important part of environmental carbon cycling, human nutrition, and industrial processes based on cellulosic bioconversion. Here we demonstrate a broadly applicable method to analyze how microbes catabolize plant polysaccharides that integrates carbohydrate-active enzyme (CAZyme) assays, RNA sequencing (RNA-seq), and anaerobic growth screening. We apply this method to study how the bacterium Clostridium phytofermentans ferments plant biomass components including glucans, mannans, xylans, galactans, pectins, and arabinans. These polysaccharides are fermented with variable efficiencies, and diauxies prioritize metabolism of preferred substrates. Strand-specific RNA-seq reveals how this bacterium responds to polysaccharides by up-regulating specific groups of CAZymes, transporters, and enzymes to metabolize the constituent sugars. Fifty-six up-regulated CAZymes were purified, and their activities show most polysaccharides are degraded by multiple enzymes, often from the same family, but with divergent rates, specificities, and cellular localizations. CAZymes were then tested in combination to identify synergies between enzymes acting on the same substrate with different catalytic mechanisms. We discuss how these results advance our understanding of how microbes degrade and metabolize plant biomass.
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Affiliation(s)
- Magali Boutard
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Tristan Cerisy
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Pierre-Yves Nogue
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | | | | | - Marcel Salanoubat
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
| | - Andrew C. Tolonen
- Genoscope, CEA, DSV, IG, Évry, France
- CNRS-UMR8030, Évry, France
- Department of Biology, Université d'Évry Val d'Essonne, Évry, France
- * E-mail:
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Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 2014; 18:853-63. [PMID: 25108363 DOI: 10.1007/s00792-014-0676-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
Abstract
Subseafloor sediment samples derived from a sediment core of 60 m length were used to enrich psychrophilic aerobic bacteria on cellulose, xylan, chitin, and starch. A variety of species belonging to Alpha- and Gammaproteobacteria and to Flavobacteria were isolated from sediment depths between 12 and 42 mbsf. Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes. More than 200 open reading frames coding for glycoside hydrolases were identified, and more than 60 of them relevant for enzymatic degradation of lignocellulose. Four genes encoding β-glucosidases with less than 52% identities to characterized enzymes were chosen for recombinant expression in Escherichia coli. In addition one endomannanase, two endoxylanases, and three β-xylosidases were produced recombinantly. All genes could be actively expressed. Functional analysis revealed discrepancies and additional variability for the recombinant enzymes as compared to the sequence-based predictions.
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Affiliation(s)
- Barbara Klippel
- Institute of Technical Microbiology, Hamburg University of Technology, Kasernenstr. 12, 21073, Hamburg, Germany
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43
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Martin M, Biver S, Steels S, Barbeyron T, Jam M, Portetelle D, Michel G, Vandenbol M. Identification and characterization of a halotolerant, cold-active marine endo-β-1,4-glucanase by using functional metagenomics of seaweed-associated microbiota. Appl Environ Microbiol 2014; 80:4958-67. [PMID: 24907332 PMCID: PMC4135742 DOI: 10.1128/aem.01194-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/29/2014] [Indexed: 11/20/2022] Open
Abstract
A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.
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Affiliation(s)
- Marjolaine Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Sophie Biver
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Sébastien Steels
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Murielle Jam
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Daniel Portetelle
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Micheline Vandenbol
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
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44
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Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ, Seymour JR. Variability in microbial community composition and function between different niches within a coral reef. MICROBIAL ECOLOGY 2014; 67:540-552. [PMID: 24477921 DOI: 10.1007/s00248-013-0362-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/26/2013] [Indexed: 06/03/2023]
Abstract
To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.
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Affiliation(s)
- Jessica Tout
- Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW, Australia,
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45
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Zhang X, Xu S, Li C, Zhao L, Feng H, Yue G, Ren Z, Cheng G. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. Res Microbiol 2014; 165:128-39. [DOI: 10.1016/j.resmic.2014.01.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/04/2014] [Indexed: 11/27/2022]
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46
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Sorokovikova EG, Belykh OI, Gladkikh AS, Kotsar OV, Tikhonova IV, Timoshkin OA, Parfenova VV. Diversity of cyanobacterial species and phylotypes in biofilms from the littoral zone of Lake Baikal. J Microbiol 2013; 51:757-65. [PMID: 24385352 DOI: 10.1007/s12275-013-3240-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/11/2013] [Indexed: 11/24/2022]
Abstract
The majority of naturally occurring biofilms contain numerous microorganisms that have not yet been cultured. Additionally, there is little information available regarding the genetic structure and species diversity of these communities. Therefore, we characterised the species diversity, structure and metagenome of biofilms grown on stones and steel plates in the littoral zone of Lake Baikal (East Siberia, Russia) by applying three different approaches. First, light microscopy enabled identification of the species diversity of biofilm-forming cyanobacteria on different substrates with the dominance of Rivularia rufescens, Tolypothrix limbata, Chamaesiphon fuscus, Ch. subglobosus, and Heteroleibleinia pusilla. Additionally, scanning electron microscopy was used to show the spatial structure of biofilms. Finally, sequence analysis of 30,660 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to Cyanobacteria (8-46% sequences), Proteobacteria (14-43%), and Bacteroidetes (10-41%). Rivularia sp., Pseudanabaena sp., and Chamaesiphon spp. were the dominant cyanobacterial phylotypes.
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Affiliation(s)
- Ekaterina G Sorokovikova
- Limnological Institute, Siberian Branch of Russian Academy of Sciences, 3, Ulan-Batorskaya, 664033, Irkutsk, Russia,
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47
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Salta M, Wharton JA, Blache Y, Stokes KR, Briand JF. Marine biofilms on artificial surfaces: structure and dynamics. Environ Microbiol 2013; 15:2879-93. [PMID: 23869714 DOI: 10.1111/1462-2920.12186] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 05/31/2013] [Accepted: 06/07/2013] [Indexed: 01/03/2023]
Abstract
The search for new antifouling (AF) coatings that are environmentally benign has led to renewed interest in the ways that micro-organisms colonize substrates in the marine environment. This review covers recently published research on the global species composition and dynamics of marine biofilms, consisting mainly of bacteria and diatoms found on man-made surfaces including AF coatings. Marine biofilms directly interact with larger organisms (macrofoulers) during colonization processes; hence, recent literature on understanding the basis of the biofilm/macrofouling interactions is essential and will also be reviewed here. Overall, differences have been identified in species composition between biofilm and planktonic forms for both diatoms and bacteria at various exposure sites. In most studies, the underlying biofilm was found to induce larval and spore settlement of macrofoulers; however, issues such as reproducibility, differences in exposure sites and biofilm composition (natural multispecies vs. monospecific species) may influence the outcomes.
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Affiliation(s)
- Maria Salta
- National Centre for Advanced Tribology at Southampton, Engineering Sciences, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Julian A Wharton
- National Centre for Advanced Tribology at Southampton (nCATS), Engineering Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Yves Blache
- MAPIEM, Biofouling et Substances Naturelles Marines, Universite du Sud Toulon-Var, La Valette-du-Var, France
| | - Keith R Stokes
- National Centre for Advanced Tribology at Southampton (nCATS), Engineering Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Physical Sciences Department, DSTL, Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Jean-Francois Briand
- MAPIEM, Biofouling et Substances Naturelles Marines, Universite du Sud Toulon-Var, La Valette-du-Var, France
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48
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Zhang XF, Zhao L, Xu SJ, Liu YZ, Liu HY, Cheng GD. Soil moisture effect on bacterial and fungal community in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types. J Appl Microbiol 2013; 114:1054-65. [PMID: 23241008 DOI: 10.1111/jam.12106] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 12/07/2012] [Accepted: 12/07/2012] [Indexed: 11/29/2022]
Abstract
AIM This study investigated the effects of environmental variables on the bacterial and fungal communities of the Beilu River (on the Tibetan Plateau) permafrost soils with different vegetation types. METHODS AND RESULTS Microbial communities were sampled from meadow, steppe and desert steppe permafrost soils during May, June, August and November, and they were analysed by both pyrosequencing and the use of Biolog EcoPlates. The dominant bacterial and fungal phyla in meadow and steppe soils were Proteobacteria and Ascomycota, whereas Actinobacteria and Basidiomycota predominated in desert steppe soils. The bacterial communities in meadow soils degraded amines and amino acids very rapidly, while polymers were degraded rapidly by steppe communities. The RDA patterns showed that the microbial communities differed greatly between meadow, steppe and desert steppe, and they were related to variations in the soil moisture, C/N ratio and pH. A UniFrac analysis detected clear differences between the desert steppe bacterial community and others, and seasonal shifts were observed. The fungal UniFrac patterns differed significantly between meadow and steppe soils. There were significant correlations between the bacterial diversity (H') and soil moisture (r = 0.506) and C/N (r = 0.527). The fungal diversity (Hf') was significantly correlated with the soil pH (r = 0.541). CONCLUSION The soil moisture, C/N ratio and pH were important determinants of the microbial community structure in Beilu River permafrost soils. SIGNIFICANCE AND IMPACT OF THE STUDY These results may provide a useful baseline for predicting the variation in microbial communities in response to climate changes.
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Affiliation(s)
- X F Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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49
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Simister R, Taylor MW, Tsai P, Fan L, Bruxner TJ, Crowe ML, Webster N. Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge, Rhopaloeides odorabile. Environ Microbiol 2012; 14:3232-46. [PMID: 23106937 DOI: 10.1111/1462-2920.12010] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/24/2012] [Accepted: 09/27/2012] [Indexed: 01/02/2023]
Abstract
Marine sponges are diverse, abundant and provide a crucial coupling point between benthic and pelagic habitats due to their high filtration rates. They also harbour extensive microbial communities, with many microbial phylotypes found exclusively in sponge hosts and not in the seawater or surrounding environment, i.e. so-called sponge-specific clusters (SCs) or sponge- and coral-specific clusters (SCCs). We employed DNA (16S rRNA gene) and RNA (16S rRNA)-based amplicon pyrosequencing to investigate the effects of sublethal thermal stress on the bacterial biosphere of the Great Barrier Reef sponge Rhopaloeides odorabile. A total of 8381 operational taxonomic units (OTUs) (97% sequence similarity) were identified, affiliated with 32 bacterial phyla from seawater samples, 23 bacterial phyla from sponge DNA extracts and 18 bacterial phyla from sponge RNA extracts. Sublethal thermal stress (31°C) had no effect on the present and/or active portions of the R. odorabile bacterial community but a shift in the bacterial assemblage was observed in necrotic sponges. Over two-thirds of DNA and RNA sequences could be assigned to previously defined SCs/SCCs in healthy sponges whereas only 12% of reads from necrotic sponges could be assigned to SCs/SCCs. A rapid decline in host health over a 1°C temperature increment suggests that sponges such as R. odorabile may be highly vulnerable to the effects of global climate change.
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Affiliation(s)
- Rachel Simister
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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50
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Seymour JR, Doblin MA, Jeffries TC, Brown MV, Newton K, Ralph PJ, Baird M, Mitchell JG. Contrasting microbial assemblages in adjacent water masses associated with the East Australian Current. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:548-555. [PMID: 23760900 DOI: 10.1111/j.1758-2229.2012.00362.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 05/30/2012] [Indexed: 06/02/2023]
Abstract
Different oceanographic provinces host discrete microbial assemblages that are adapted to local physicochemical conditions. We sequenced and compared the metagenomes of two microbial communities inhabiting adjacent water masses in the Tasman Sea, where the recent strengthening of the East Australian Current (EAC) has altered the ecology of coastal environments. Despite the comparable latitude of the samples, significant phylogenetic differences were apparent, including shifts in the relative frequency of matches to Cyanobacteria, Crenarchaeota and Euryarchaeota. Fine-scale variability in the structure of SAR11, Prochlorococcus and Synechococcus populations, with more matches to 'warm-water' ecotypes observed in the EAC, indicates the EAC may drive an intrusion of tropical microbes into temperate regions of the Tasman Sea. Furthermore, significant shifts in the relative importance of 17 metabolic categories indicate that the EAC prokaryotic community has different physiological properties than surrounding waters.
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Affiliation(s)
- Justin R Seymour
- Plant Functional Biology & Climate Change Cluster, University of Technology, PO Box 123, Broadway, Sydney, NSW, 2007, Australia
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