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Fang G, Yu H, Sheng H, Tang Y, Liang Z. Comparative analysis of microbial communities between water and sediment in Laoshan Bay marine ranching with varied aquaculture activities. MARINE POLLUTION BULLETIN 2021; 173:112990. [PMID: 34634629 DOI: 10.1016/j.marpolbul.2021.112990] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 06/13/2023]
Abstract
We profiled and compared the bacterial and protist community compositions and dynamics in the Laoshan Bay marine ranching involving varied aquaculture activities. The dominant species, differential species and community compositions among the five aquaculture areas, two habitats and two periods were significantly different. The relationships between microbial communities and environmental factors were analyzed. We found that microbial communities in the water were more sensitive to the environmental changes than sediment, and the responses of bacterial and protist communities to the disturbances were varied. To meet the challenges of higher aquaculture density, the proportion of the positive correlations among co-occurrence networks in the water increased markedly from July to November; while the positive proportion in the sediment was stable. Potential ecological interactions and keystone taxa between bacteria and protists were studied. These results advanced our understanding of how mariculture stressors affect microbial communities in marine ranching.
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Affiliation(s)
- Guangjie Fang
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Haolin Yu
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Huaxiang Sheng
- Fisheries College, Ocean University of China, Qingdao 266002, China
| | - Yanli Tang
- Fisheries College, Ocean University of China, Qingdao 266002, China.
| | - Zhenlin Liang
- Marine College, Shandong University, Weihai 264200, China
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2
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Variation of Microbial Communities in Aquatic Sediments under Long-Term Exposure to Decabromodiphenyl Ether and UVA Irradiation. SUSTAINABILITY 2019. [DOI: 10.3390/su11143773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were evaluated in order to assess their influence on the bacterial community. The dominant bacterial community in a single stress situation, i.e., exposure to BDE-209 include members of Comamonadaceae, members of Xanthomonadaceae, a Pseudomonas sp. and a Hydrogenophaga sp. Such bacteria are capable of biodegrading polybrominated diphenyl ethers (PBDEs). When multiple environmental stresses were present, Acidobacteria bacterium and a Terrimonas sp. were predominant, which equipped the population with multiple physiological characteristics that made it capable of both PBDE biodegradation and resistance to UVA irradiation. Methloversatilis sp. and Flavisolibacter sp. were identified as representative genera in this population that were radioresistant. In addition to the above, sediment heterogeneity is also able to alter bacterial community diversity. In total, seventeen species of bacteria were identified in the microcosms containing more clay particles and higher levels of soil organic matter (SOM). This means that these communities are more diverse than in microcosms that contained more sand particles and a lower SOM, which were found to have only twelve identifiable bacterial species. This is the first report to evaluate how changes in bacterial communities in aquatic sediment are affected by the presence of multiple variable environmental factors at the same time.
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Fitch A, Orland C, Willer D, Emilson EJS, Tanentzap AJ. Feasting on terrestrial organic matter: Dining in a dark lake changes microbial decomposition. GLOBAL CHANGE BIOLOGY 2018; 24:5110-5122. [PMID: 29998600 PMCID: PMC6220883 DOI: 10.1111/gcb.14391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/30/2018] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses. We found that bacterial production (BP) decreased across lakes with aromatic dissolved organic matter (DOM) in sediment pore water, but the process underlying this pattern differed between lakes. Bacteria in the dark lake invested in the energetically costly production of extracellular enzymes as aromatic DOM increased in availability in the sediments. By contrast, bacteria in the clear lake may have lacked the nutrients and/or genetic potential to degrade aromatic DOM and instead mineralized photo-degraded OM into CO2 . The two lakes differed in community composition, with concentrations of dissolved organic carbon and pH differentiating microbial assemblages. Furthermore, functional genes relating to t-OM degradation were relatively higher in the dark lake. Our results suggest that future changes in t-OM inputs to lake sediments will have different effects on carbon cycling depending on the potential for photo-degradation of OM and composition of resident bacterial communities.
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Affiliation(s)
- Amelia Fitch
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Chloe Orland
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - David Willer
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Erik J. S. Emilson
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
- Natural Resources Canada, Great Lakes Forestry CentreSault Ste. MarieOntario
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4
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Duffy DJ, Schnitzler C, Karpinski L, Thomas R, Whilde J, Eastman C, Yang C, Krstic A, Rollinson D, Zirkelbach B, Yetsko K, Burkhalter B, Martindale MQ. Sea turtle fibropapilloma tumors share genomic drivers and therapeutic vulnerabilities with human cancers. Commun Biol 2018; 1:63. [PMID: 30271945 PMCID: PMC6123702 DOI: 10.1038/s42003-018-0059-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
Wildlife populations are under intense anthropogenic pressures, with the geographic range of many species shrinking, dramatic reductions in population numbers and undisturbed habitats, and biodiversity loss. It is postulated that we are in the midst of a sixth (Anthropocene) mass extinction event, the first to be induced by human activity. Further, threatening vulnerable species is the increased rate of emerging diseases, another consequence of anthropogenic activities. Innovative approaches are required to help maintain healthy populations until the chronic underlying causes of these issues can be addressed. Fibropapillomatosis in sea turtles is one such wildlife disease. Here, we applied precision-medicine-based approaches to profile fibropapillomatosis tumors to better understand their biology, identify novel therapeutics, and gain insights into viral and environmental triggers for fibropapillomatosis. We show that fibropapillomatosis tumors share genetic vulnerabilities with human cancer types, revealing that they are amenable to treatment with human anti-cancer therapeutics. David Duffy et al. use a precision-medicine-based approach to study fibropapillomatosis tumors in sea turtles to identify environmental triggers and potential therapeutics. They show that these tumors share genetic similarities with human cancer types, and may be treatable using human anti-cancer therapies.
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Affiliation(s)
- David J Duffy
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA. .,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK. .,Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland.
| | - Christine Schnitzler
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Lorraine Karpinski
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA.,Pinecrest Veterinary Hospital, 12125 South Dixie Highway, Pinecrest, FL, 33156, USA
| | - Rachel Thomas
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Jenny Whilde
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Catherine Eastman
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Calvin Yang
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Aleksandar Krstic
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Devon Rollinson
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Bette Zirkelbach
- The Turtle Hospital, 2396 Overseas Highway, Marathon, FL, 33050, USA
| | - Kelsey Yetsko
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Brooke Burkhalter
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, Sea Turtle Hospital, University of Florida, St. Augustine, FL, 32080, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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5
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Hunting ER, Barmentlo SH, Schrama M, van Bodegom PM, Zhai Y, Vijver MG. Agricultural constraints on microbial resource use and niche breadth in drainage ditches. PeerJ 2017; 5:e4175. [PMID: 29302393 PMCID: PMC5742521 DOI: 10.7717/peerj.4175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/29/2017] [Indexed: 11/20/2022] Open
Abstract
Background Microorganisms govern important ecosystems processes, in particular the degradation of organic matter (OM). However, microorganisms are rarely considered in efforts to monitor ecosystem health and functioning. Evidence suggests that environmental perturbations can adversely affect microbial communities and their ability to use available substrates. However, whether impacted microbial efficiencies in extracting and utilizing the available resources (resource niche breadth) translate to changes in OM degradation in natural systems remains poorly understood. Methods Here we evaluated effects of differences in OM related to agricultural land use (OM derived from ditches adjacent to grasslands, bulb fields and a pristine dune area) on microbial functioning. We specifically assessed (1) resource niche breadths of microbial communities during initial community assembly in laboratory microcosms and already established natural communities, and (2) how changes in community resource niche breadth translates to the degradation of natural OM. Results A disparity existed between microbial resource niche breadth in laboratory incubations and natural microbial communities. Resource utilization and niche breadth of natural microbial communities was observed to be constrained in drainage ditches adjacent to agricultural fields. This outcome coincides with retarded degradation of natural OM collected from ditches adjacent to hyacinth bulb fields. Microbial communities in bulb field ditches further showed functional redundancy when offered grassland OM of seemingly higher substrate quality. Discussion Results presented in this study suggest that agricultural practices can impose constraints on microbial functional diversity by reducing OM resource quality, which can subsequently translate to confined microbial resource niche differentiation and reduced organic matter degradation rates. This hints that assessments of actual microbial resource utilization and niche differentiation could potentially be used to assess the ecological health and functioning of natural communities.
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Affiliation(s)
- Ellard R Hunting
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - S Henrik Barmentlo
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - Maarten Schrama
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands.,NIOO-KNAW, Wageningen, The Netherlands
| | | | - Yujia Zhai
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences, Leiden University, Leiden, Netherlands
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6
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Zhai Y, Hunting ER, Wouterse M, Peijnenburg WJGM, Vijver MG. Importance of exposure dynamics of metal-based nano-ZnO, -Cu and -Pb governing the metabolic potential of soil bacterial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 145:349-358. [PMID: 28759764 DOI: 10.1016/j.ecoenv.2017.07.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/11/2017] [Accepted: 07/15/2017] [Indexed: 06/07/2023]
Abstract
Metal-based engineered nanomaterials (ENMs) are known to affect bacterial processes and metabolic activities. While testing their negative effects on biological components, studies traditionally rely on initial exposure concentrations and thereby do not take into consideration the dynamic behavior of ENMs that ultimately determines exposure and toxicity (e.g. ion release). Moreover, functional responses of soil microbial communities to ENMs exposure can be caused by both the particulate forms and the ionic forms, yet their relative contributions remain poorly understood. Therefore, we investigated the dynamic changes of exposure concentrations of three different types of ENMs (nano-ZnO, -Cu and -Pb) and submicron particles (SMPs) in relation to their impact on the capacity of soil bacterial communities to utilize carbon substrates. The different ENMs were chosen to differ in dissolution potential. The dynamic exposures of ENMs were considered using a time weighted average (TWA) approach. The joint toxicity of the particulate forms and the ionic forms of ENMs was evaluated using a response addition model. Our results showed that the effect concentrations of spherical nano-ZnO, -Cu and SMPs, and Pb-based perovskites expressed as TWA were lower than expressed as initial concentrations. Both particulate forms and ionic forms of spherical 18nm, 43nm nano-ZnO and 50nm, 100nm nano-Cu contribute to the overall response at the EC50 levels. The particulate forms for 150nm, 200nm and 900nm ZnO SMPs and rod-shaped 78nm nano-Cu mainly affected the soil microbial metabolic potential, while the Cu ions released from spherical 25nm nano-Cu, 500nm Cu SMPs and Pb ions released from perovskites mainly described the effects to bacterial communities. Our results indicate that the dynamic exposure of ENMs and relative contributions of particles and ions require consideration in order to pursue a naturally realistic assessment of environmental risks of metal-based ENMs.
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Affiliation(s)
- Yujia Zhai
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA, Leiden, The Netherlands.
| | - Ellard R Hunting
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA, Leiden, The Netherlands
| | - Marja Wouterse
- National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, The Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA, Leiden, The Netherlands; National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, The Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA, Leiden, The Netherlands
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Percak-Dennett E, He S, Converse B, Konishi H, Xu H, Corcoran A, Noguera D, Chan C, Bhattacharyya A, Borch T, Boyd E, Roden EE. Microbial acceleration of aerobic pyrite oxidation at circumneutral pH. GEOBIOLOGY 2017; 15:690-703. [PMID: 28452176 DOI: 10.1111/gbi.12241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH. Here, we describe two enrichment cultures, obtained from pyrite-bearing subsurface sediments, that were capable of sustained cell growth linked to pyrite oxidation and sulfate generation at neutral pH. The cultures were dominated by two Rhizobiales species (Bradyrhizobium sp. and Mesorhizobium sp.) and a Ralstonia species. Shotgun metagenomic sequencing and genome reconstruction indicated the presence of Fe and S oxidation pathways in these organisms, and the presence of a complete Calvin-Benson-Bassham CO2 fixation system in the Bradyrhizobium sp. Oxidation of pyrite resulted in thin (30-50 nm) coatings of amorphous Fe(III) oxide on the pyrite surface, with no other secondary Fe or S phases detected by electron microscopy or X-ray absorption spectroscopy. Rates of microbial pyrite oxidation were approximately one order of magnitude higher than abiotic rates. These results demonstrate the ability of aerobic microbial activity to accelerate pyrite oxidation and expand the potential contribution of micro-organisms to continental sulfide mineral weathering around the time of the Great Oxidation Event to include neutral-pH environments. In addition, our findings have direct implications for the geochemistry of modern sedimentary environments, including stimulation of the early stages of acid mine drainage formation and mobilization of pyrite-associated metals.
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Affiliation(s)
- E Percak-Dennett
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - S He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Konishi
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - H Xu
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - A Corcoran
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - D Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - C Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, USA
| | - A Bhattacharyya
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - T Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - E Boyd
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT, USA
| | - E E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
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Bletz MC, Archer H, Harris RN, McKenzie VJ, Rabemananjara FCE, Rakotoarison A, Vences M. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar. Front Microbiol 2017; 8:1530. [PMID: 28861051 PMCID: PMC5563069 DOI: 10.3389/fmicb.2017.01530] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/28/2017] [Indexed: 12/30/2022] Open
Abstract
Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance.
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Affiliation(s)
- Molly C Bletz
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Holly Archer
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | - Reid N Harris
- Department of Biology, James Madison University, HarrisonburgVA, United States
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado BoulderBoulder, CO, United States
| | | | - Andolalao Rakotoarison
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany.,Mention Biologie et Biodiversité Animale, University of AntananarivoAntananarivo, Madagascar
| | - Miguel Vences
- Zoological Institute, Technical University of BraunschweigBraunschweig, Germany
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Al-Jassim N, Mantilla-Calderon D, Wang T, Hong PY. Inactivation and Gene Expression of a Virulent Wastewater Escherichia coli Strain and the Nonvirulent Commensal Escherichia coli DSM1103 Strain upon Solar Irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3649-3659. [PMID: 28263596 DOI: 10.1021/acs.est.6b05377] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This study examined the decay kinetics and molecular responses of two Escherichia coli strains upon solar irradiation. The first is E. coli PI-7, a virulent and antibiotic-resistant strain that was isolated from wastewater and carries the emerging NDM-1 antibiotic resistance gene. The other strain, E. coli DSM1103, displayed lower virulence and antibiotic resistance than E. coli PI-7. In a buffer solution, E. coli PI-7 displayed a longer lag phase prior to decay and a longer half-life compared with E. coli DSM1103 (6.64 ± 0.63 h and 2.85 ± 0.46 min vs 1.33 ± 0.52 h and 2.04 ± 0.36 min). In wastewater, both E. coli strains decayed slower than they did in buffer. Although solar irradiation remained effective in reducing the numbers of both strains by more than 5-log10 in <24 h, comparative genomics and transcriptomics revealed differences in the genomes and overall regulation of genes between the two E. coli strains. A wider arsenal of genes related to oxidative stress, cellular repair and protective mechanisms were upregulated in E. coli PI-7. Subpopulations of E. coli PI-7 expressed genes related to dormancy and persister cell formation during the late decay phase, which may have accounted for its prolonged persistence. Upon prolonged solar irradiation, both E. coli strains displayed upregulation of genes related to horizontal gene transfer and antibiotic resistance. Virulence functions unique to E. coli PI-7 were also upregulated. Our findings collectively indicated that, whereas solar irradiation is able to reduce total cell numbers, viable E. coli remained and expressed genes that enable survival despite solar treatment. There remains a need for heightened levels of concern regarding risks arising from the dissemination of E. coli that may remain viable in wastewater after solar irradiation.
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Affiliation(s)
- Nada Al-Jassim
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center (WDRC), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Saudi Arabia
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10
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Gamalier JP, Silva TP, Zarantonello V, Dias FF, Melo RC. Increased production of outer membrane vesicles by cultured freshwater bacteria in response to ultraviolet radiation. Microbiol Res 2017; 194:38-46. [DOI: 10.1016/j.micres.2016.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/24/2016] [Accepted: 08/03/2016] [Indexed: 11/28/2022]
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11
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Zhai Y, Hunting ER, Wouters M, Peijnenburg WJGM, Vijver MG. Silver Nanoparticles, Ions, and Shape Governing Soil Microbial Functional Diversity: Nano Shapes Micro. Front Microbiol 2016; 7:1123. [PMID: 27504108 PMCID: PMC4959451 DOI: 10.3389/fmicb.2016.01123] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2016] [Indexed: 11/29/2022] Open
Abstract
Silver nanoparticles (AgNPs) affect microbial metabolic processes at single cell level or lab-culture strains. However, the impact of different AgNPs properties such as the particle, ion release, and shape on functional responses of natural soil microbial communities remain poorly understood. Therefore, we assessed the relative importance of particles and ions of AgNPs in bacterial toxicity and how the functional diversity of soil microbial communities were impacted by AgNPs shapes (i.e., plates, spheres, and rods) in laboratory incubations. Our results showed that the relative contribution of AgNPs(particle) increased with increasing exposure concentrations (accounted for about 60–68% of the total toxicity at the highest exposure level). In addition, the functional composition of the microbial community differed significantly according to different AgNPs shapes. The various properties of AgNPs thus can significantly and differentially affect the functional composition of microbial communities and associated ecosystem processes depending on the level of environmental exposure.
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Affiliation(s)
- Yujia Zhai
- Institute of Environmental Sciences, Leiden University Leiden, Netherlands
| | - Ellard R Hunting
- Institute of Environmental Sciences, Leiden University Leiden, Netherlands
| | - Marja Wouters
- National Institute of Public Health and the Environment Bilthoven, Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences, Leiden UniversityLeiden, Netherlands; National Institute of Public Health and the EnvironmentBilthoven, Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences, Leiden University Leiden, Netherlands
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12
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Lü C, Wang B, He J, Vogt RD, Zhou B, Guan R, Zuo L, Wang W, Xie Z, Wang J, Yan D. Responses of Organic Phosphorus Fractionation to Environmental Conditions and Lake Evolution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5007-5016. [PMID: 27104794 DOI: 10.1021/acs.est.5b05057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Geochemical fractionation is used to assess the significance of environmental factors on organic phosphorus (OP) pools in sediments. Labile, moderately labile, and nonlabile OP pools in the sediments from Lake Hulun, Inner Mongolia, were fractionated, and their responses to environmental conditions and lake evolution were investigated based on the spatial and vertical distribution of OP fractionations. In light of the recalcitrant characteristics of organic matter (OM) in different environmental conditions, the pH presents significant negative effects on the amount of labile OP, while water depth shows an important role in regulating the distribution between the moderately labile and nonlabile OP pools. A latitudinal zonation in the distribution of OP pools in surface sediments from different lakes was apparent with this zonation likely linked to the gradient effects of climate and anthropogenic activities on OM decomposition and thereby on the sediments capacity to hold phosphorus. These results show that OM plays a role in governing the impacts of weather and environmental factors on OP fractionation in aquatic environments. This work suggests that OP pools in the sediment core could be used as an archive for environmental conditions and lake evolution.
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Affiliation(s)
- Changwei Lü
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
- Institute of Environmental Geology, Inner Mongolia University , Huhhot 010021, China
- Department of Chemistry, University of Oslo , N-0315, Oslo, Norway
| | - Bing Wang
- Forestry College, Inner Mongolia Agricultural University , Huhhot 010019, China
| | - Jiang He
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
- Institute of Environmental Geology, Inner Mongolia University , Huhhot 010021, China
| | - Rolf D Vogt
- Department of Chemistry, University of Oslo , N-0315, Oslo, Norway
| | - Bin Zhou
- Department of Chemistry, University of Oslo , N-0315, Oslo, Norway
- Tianjin Academy of Environmental Sciences , Tianjin, 300191, China
| | - Rui Guan
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
| | - Le Zuo
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
| | - Weiying Wang
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
| | - Zhilei Xie
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
| | - Jinghua Wang
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
| | - Daohao Yan
- College of Environment and Resources, Inner Mongolia University , Huhhot 010021, China
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13
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Effects of agricultural practices on organic matter degradation in ditches. Sci Rep 2016; 6:21474. [PMID: 26892243 PMCID: PMC4759819 DOI: 10.1038/srep21474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/25/2016] [Indexed: 11/24/2022] Open
Abstract
Agricultural practices can result in differences in organic matter (OM) and agricultural chemical inputs in adjacent ditches, but its indirect effects on OM composition and its inherent consequences for ecosystem functioning remain uncertain. This study determined the effect of agricultural practices (dairy farm grasslands and hyacinth bulb fields) on OM degradation by microorganisms and invertebrates with a consumption and food preference experiment in the field and in the laboratory using natural OM collected from the field. Freshly cut grass and hyacinths were also offered to control for OM composition and large- and small mesh-sizes were used to distinguish microbial decomposition and invertebrate consumption. Results show that OM decomposition by microorganisms and consumption by invertebrates was similar throughout the study area, but that OM collected from ditches adjacent grasslands and freshly cut grass and hyacinths were preferred over OM collected from ditches adjacent to a hyacinth bulb field. In the case of OM collected from ditches adjacent hyacinth bulb fields, both microbial decomposition and invertebrate consumption were strongly retarded, likely resulting from sorption and accumulation of pesticides. This outcome illustrates that differences in agricultural practices can, in addition to direct detrimental effects on aquatic organisms, indirectly alter the functioning of adjacent aquatic ecosystems.
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14
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Bacosa HP, Liu Z, Erdner DL. Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters. Front Microbiol 2015; 6:1325. [PMID: 26648916 PMCID: PMC4664628 DOI: 10.3389/fmicb.2015.01325] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/11/2015] [Indexed: 01/06/2023] Open
Abstract
Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.
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Affiliation(s)
- Hernando P Bacosa
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
| | - Deana L Erdner
- Marine Science Institute, The University of Texas at Austin Port Aransas, TX, USA
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15
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Oni OE, Schmidt F, Miyatake T, Kasten S, Witt M, Hinrichs KU, Friedrich MW. Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea. Front Microbiol 2015; 6:1290. [PMID: 26635758 PMCID: PMC4658423 DOI: 10.3389/fmicb.2015.01290] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/04/2015] [Indexed: 01/05/2023] Open
Abstract
The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30-530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments.
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Affiliation(s)
- Oluwatobi E Oni
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany ; MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany ; International Max-Planck Research School for Marine Microbiology Bremen, Germany
| | - Frauke Schmidt
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Tetsuro Miyatake
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany
| | - Sabine Kasten
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany ; Department of Marine Geochemistry, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Michael W Friedrich
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany ; MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
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16
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Effects of cultivation of OsrHSA transgenic rice on functional diversity of microbial communities in the soil rhizosphere. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.cj.2014.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Hunting ER, Vijver MG, van der Geest HG, Mulder C, Kraak MHS, Breure AM, Admiraal W. Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms. Front Microbiol 2015; 6:105. [PMID: 25759686 PMCID: PMC4338809 DOI: 10.3389/fmicb.2015.00105] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/27/2015] [Indexed: 01/01/2023] Open
Abstract
Decomposition of organic matter is an important ecosystem process governed in part by bacteria. The process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. However, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. Therefore, this study aims to evaluate the effect of an increase in bacterial community resemblance on both decomposition and the stability of bacterial metabolism in aquatic sediments. To this end, we performed laboratory microcosm experiments in which we examined the influence of bacterial consortia differing in number and composition of species on bacterial activity (Electron Transport System Activity, ETSA), dissolved organic carbon production and wavelet transformed measurements of redox potential (Eh). Single substrate affinities of the individual bacterial species were determined in order to calculate the metabolic diversity of the microbial community. Results presented here indicate that bacterial activity and organic matter decomposition increase with widening of the resource niche breadth, and that metabolic stability increases with increasing overlap in bacterial resource niches, hinting that resource niche overlap can promote the stability of bacterial community metabolism.
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Affiliation(s)
- Ellard R Hunting
- Department of Conservation Biology, Institute of Environmental Sciences (CML), Leiden University Leiden, Netherlands
| | - Martina G Vijver
- Department of Conservation Biology, Institute of Environmental Sciences (CML), Leiden University Leiden, Netherlands
| | - Harm G van der Geest
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
| | - Christian Mulder
- National Institute for Public Health and the Environment (RIVM-LER) - Centre for Sustainability, Environment and Health Bilthoven, Netherlands
| | - Michiel H S Kraak
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
| | - Anton M Breure
- National Institute for Public Health and the Environment (RIVM-LER) - Centre for Sustainability, Environment and Health Bilthoven, Netherlands ; Department of Environmental Science, Institute for Water and Wetland Research, Radboud University Nijmegen, Netherlands
| | - Wim Admiraal
- Department of Aquatic Ecology and Ecotoxicology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
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