1
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Tang J, Zuo W, Guo L, Han Z, Yang C, Han B, Dai L, Zhang X, Zhou X. Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 2024; 15:6937. [PMID: 39138170 PMCID: PMC11322527 DOI: 10.1038/s41467-024-51365-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.
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Affiliation(s)
- Junbo Tang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Zhihao Han
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Microbiology and Immunology, College of Biological Science, China Agricultural University, Beijing, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Hainan, China.
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2
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Zhang H, Hu W, Liu R, Bartlam M, Wang Y. Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes. Environ Microbiol 2023; 25:3703-3718. [PMID: 37964717 DOI: 10.1111/1462-2920.16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Wei Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Ruidan Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin, China
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3
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Shan X, Guo H, Ma F, Shan Z. Enhanced treatment of synthetic wastewater by bioaugmentation with a constructed consortium. CHEMOSPHERE 2023; 338:139520. [PMID: 37454986 DOI: 10.1016/j.chemosphere.2023.139520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Bioaugmentation by adding well-functioning mixed microorganism consortia represents a potentially useful approach to improve contaminant removal in wastewater treatment plants (WWTPs). However, unfavorable environmental conditions (i.e., low temperatures) can severely inhibit microbial activity, drawing our attention to constructing cold-tolerant microorganism preparations and investigating their availability in practical applications. Here we screened four in situ functional isolates from the activated sludge of secondary sedimentation tanks in WWTPs to construct a psychrophilic microbial consortium, which was used to perform bioaugmentation for enhanced removal of nitrogen and phosphorus under low temperatures. The consortium was established by cocultivation of four isolates, characterized by 16 S rRNA as the COD-degrading bacterium Aeromonas sp. Z3, aerobic denitrifying bacterium Acinetobacter sp. HF9, nitrifying bacterium Klebsiella sp. X8, and polyphosphate-accumulating bacterium Pseudomonas sp. PC5 respectively. The microorganism preparation was composed of Z3, HF9, X8, and PC5 under the ratio of 1: 1: 3: 1, which can exert optimal pollutant removal under the conditions of 12 °C, 6.0-9.0 pH, 120-200 r‧min-1, and a dosage of 5% (V/V). A 30-day continuous operation of the bioaugmented and control sequencing batch reactors (SBRs) was investigated, and the bioaugmented SBR showed a shorter start-up stage and a more stable operating situation. Compared to the control SBR, the COD, NH4+-N, TN, and TP removal efficiency of the bioaugmented SBR increased by an average of 7.95%, 9.05%, 9.54%, and 7.45% respectively. The analysis of the microbial community revealed that the introduced isolates were dominant in the activated sludge and that functional taxa such as Proteobacteria, Bacteroidota, and Actinobacteria were further enriched after a period of bioaugmentation. The study provides some basis and guidance for the practical application of how to strengthen the stable operation of WWTPs under low temperatures.
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Affiliation(s)
- Xiaoqing Shan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Haijuan Guo
- School of Environment, Liaoning University, Shenyang, 110036, PR China.
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; School of Environment, Liaoning University, Shenyang, 110036, PR China.
| | - Zelin Shan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
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4
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Zheng WL, Wang YF, Mo J, Zeng P, Chen J, Sun C. Effects of biochar application and nutrient fluctuation on the growth, and cadmium and nutrient uptake of Trifolium repens with different planting densities in Cd-contaminated soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1269082. [PMID: 37799556 PMCID: PMC10548119 DOI: 10.3389/fpls.2023.1269082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
Biochar has been used to remediate contaminated-soil with heavy metals, however, less is known on how biochar interacts with planting density and nutrient fluctuation to affect the remediation. A pot experiment was conducted in the greenhouse to investigate the effects of biochar application (without vs. with 1% biochar, g/g substrate), nutrient fluctuation (constant vs. pulsed) and planting density (1-, 3- and 6-individuals per pot) on the growth, and cadmium (Cd) and nutrient uptake of Trifolium repens population. Our results found that the growth of T. repens population increased significantly with increasing planting density, and the increment decreased with increasing planting density. Both the Cd and nutrient uptake were higher at higher planting density (e.g., 3- and 6-individuals) than at lower planting density (e.g., 1-individual). Biochar application increased the biomass and shoot Cd uptake, but decreased the ratio of root to shoot and root Cd uptake of T. repens population, the effects of which were significantly influenced by planting density. Although nutrient fluctuation had no effect on the growth of T. repens population, but its interaction with planting density had significant effects on Cd uptake in tissues. Overall, the effects of biochar application and nutrient fluctuation on the growth and Cd uptake were both influenced by planting density in the present study. Our findings highlight that biochar application and constant nutrient supply at an appropriate planting density, such as planting density of 3-individuals per pot in the present study, could promote the growth, and Cd and nutrient uptake of T. repens population.
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Affiliation(s)
- Wei-Long Zheng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, China
| | - Yan-Fei Wang
- Taizhou Institute of Product Quality and Safety Inspection, Taizhou, China
| | - Jingya Mo
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, China
| | - Pu Zeng
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, China
| | - Jiayi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, China
| | - Chenliang Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou, China
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5
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy University of Gothenburg Gothenburg Sweden
| | - Melle Säve‐Söderbergh
- Science Division Swedish Food Agency Uppsala Sweden
- Institute of Environmental Medicine, Karolinska Institutet Stockholm Sweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public Health Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
- Department of Ecology and Environmental Science (EMG) Umeå University Umeå Sweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research Agency Umeå Sweden
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6
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Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. THE ISME JOURNAL 2022; 16:2144-2159. [PMID: 35717467 PMCID: PMC9381525 DOI: 10.1038/s41396-022-01255-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
AbstractMicrobe–microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM’s followed the Taylor’s power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.
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7
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Sun F, Mellage A, Wang Z, Bakkour R, Griebler C, Thullner M, Cirpka OA, Elsner M. Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4050-4061. [PMID: 35263099 PMCID: PMC8988295 DOI: 10.1021/acs.est.1c05259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/24/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (μg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.
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Affiliation(s)
- Fengchao Sun
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Adrian Mellage
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstraße 94, 72076, Tübingen, Germany
| | - Zhe Wang
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Ecological Microbiology, University of
Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
- School
of Life Sciences, Technical University of
Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Rani Bakkour
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Christian Griebler
- Department
of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Thullner
- Department
of Environmental Microbiology, UFZ—Helmholtz
Centre for Environmental Research, Permoserstr. 15, 30418 Leipzig, Germany
| | - Olaf A. Cirpka
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstraße 94, 72076, Tübingen, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
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8
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Zhou R, Hou D, Zeng S, Wei D, Yu L, Bao S, Weng S, He J, Huang Z. Sedimentary Nitrogen and Sulfur Reduction Functional-Couplings Interplay With the Microbial Community of Anthropogenic Shrimp Culture Pond Ecosystem. Front Microbiol 2022; 13:830777. [PMID: 35308336 PMCID: PMC8931606 DOI: 10.3389/fmicb.2022.830777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
Sediment nitrogen and sulfur cycles are essential biogeochemical processes that regulate the microbial communities of environmental ecosystems, which have closely linked to environment ecological health. However, their functional couplings in anthropogenic aquaculture sedimentary ecosystems remain poorly understood. Here, we explored the sediment functional genes in shrimp culture pond ecosystems (SCPEs) at different culture stages using the GeoChip gene array approach with 16S amplicon sequencing. Dissimilarity analysis showed that the compositions of both functional genes and bacterial communities differed at different phases of shrimp culture with the appearance of temporal distance decay (p < 0.05). During shrimp culture, the abundances of nitrite and sulfite reduction functional genes decreased (p < 0.05), while those of nitrate and sulfate reduction genes were enriched (p < 0.05) in sediments, implying the enrichment of nitrites and sulfites from microbial metabolism. Meanwhile, nitrogen and sulfur reduction genes were found to be linked with carbon degradation and phosphorous metabolism (p < 0.05). The influence pathways of nutrients were demonstrated by structural equation modeling through environmental factors and the bacterial community on the nitrogen and sulfur reduction functions, indicating that the bacterial community response to environmental factors was facilitated by nutrients, and led to the shifts of functional genes (p < 0.05). These results indicate that sediment nitrogen and sulfur reduction functions in SCPEs were coupled, which are interconnected with the SCPEs bacterial community. Our findings will be helpful for understanding biogeochemical cycles in anthropogenic aquaculture ecosystems and promoting sustainable management of sediment environments through the framework of an ecological perspective.
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Affiliation(s)
- Renjun Zhou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongwei Hou
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shenzheng Zeng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dongdong Wei
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lingfei Yu
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shicheng Bao
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaoping Weng
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianguo He
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Jianguo He,
| | - Zhijian Huang
- State Key Laboratory of Biocontrol, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
- Zhijian Huang,
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9
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Direct evidence for deterministic assembly of bacterial communities in full-scale municipal wastewater treatment facilities. Appl Environ Microbiol 2021; 87:e0108621. [PMID: 34347524 DOI: 10.1128/aem.01086-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study we investigated whether bacterial community composition in full-scale wastewater treatment bioreactors can be better explained by niche- or neutral- based theory (deterministic or stochastic) and whether bioreactor design (continuous-flow vs. fill-and-draw) affected community assembly. Four wastewater treatment facilities (one with quadruplicated continuous-flow bioreactors, two with one continuous-flow bioreactor each, one with triplicated fill-and-draw bioreactors) were investigated. Bioreactor community composition was characterized by sequencing of PCR-amplified 16S rRNA gene fragments. Replicate bioreactors at the same wastewater treatment facility had largely reproducible (i.e., deterministic) bacterial community composition, although bacterial community composition in continuous-flow bioreactors was significantly more reproducible (P < 0.001) than in fill-and-draw bioreactors (Bray-Curtis dissimilarity: μ = 0.48 ± 0.06 vs. 0.58 ± 0.08). Next, we compared our results to previously-used indirect methods for distinguishing between deterministic and stochastic community assembly mechanisms. Synchronicity was observed in the bacterial community composition among bioreactors within the same metropolitan region, consistent with deterministic community assembly. Similarly, a null model-based analysis also indicated that all wastewater bioreactor communities were controlled by deterministic factors and that continuous-flow bioreactors were significantly more deterministic (P < 0.001) than fill-and-draw bioreactors (nearest-taxon index: μ = 3.3 ± 0.6 vs. 2.7 ± 0.8). Our results indicate that bacterial community composition in wastewater treatment bioreactors is better explained by deterministic community assembly theory; simultaneously, our results validate previously-used but indirect methods to quantify whether microbial communities were assembled via deterministic or stochastic mechanisms. IMPORTANCE Understanding the mechanisms of bacterial community assembly is one of the grand challenges of microbial ecology. In environmental systems, this challenge is exacerbated because "replicate" experiments are typically impossible; that is, microbial ecologists cannot fabricate multiple field-scale experiments of identical, natural ecosystems. Our results directly demonstrate that deterministic mechanisms are more prominent than stochastic mechanisms in the assembly of wastewater treatment bioreactor communities. Our results also suggest that wastewater treatment bioreactor design is pertinent, such that the imposition of feast-famine conditions (i.e., fill-and-draw bioreactors) nudge bacterial community assembly more towards stochastic mechanisms compared to the imposition of stringent nutrient limitation (i.e., continuous-flow bioreactors). Our research also validates the previously-used indirect methods (synchronous community dynamics and an application of a null-model) for characterizing the relative importance of deterministic versus stochastic mechanisms of community assembly.
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10
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Vizzo JI, Cabrerizo MJ, Helbling EW, Villafañe VE. Extreme and gradual rainfall effects on winter and summer estuarine phytoplankton communities from Patagonia (Argentina). MARINE ENVIRONMENTAL RESEARCH 2021; 163:105235. [PMID: 33338796 DOI: 10.1016/j.marenvres.2020.105235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Rainfall events bring both, terrigenous materials (including DOM) and nutrients to the aquatic system (e.g., via riverine runoff) having potential effects on the structure and metabolism of the phytoplankton communities. As extreme rainfall events in Patagonia occurred more frequently in the last decade (2010-2019) as compared to the previous ones (1972-2009), we exposed winter and summer phytoplankton communities (using microcosms) to solar radiation, simulating two rainfall conditions - a single extreme vs. intermittent i.e., with gradual inputs, and we assessed their photosynthetic and growth rates responses and taxonomic changes. Rainfall scenarios significantly increased growth of both communities, mainly of small nanoplanktonic species, as compared to the control. Small nanoplanktonic centric diatoms increased and dominated in both rainfall scenarios, as compared to the control, during winter and summer, with significantly smaller cells during summer as compared to winter. Photosynthetic efficiency increased in both rainfall scenarios at the end of the experiment as compared to the control. Overall, the change towards small cells (associated to rainfall events) that can use more effectively solar radiation and nutrients (as compared to large cells) may have a significant impact on the trophic webs of the South West Atlantic Ocean by favoring grazing pressure by microzooplankton, especially during summer.
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Affiliation(s)
- Juan I Vizzo
- Estación de Fotobiología Playa Unión, Casilla de Correos 15, 9103, Rawson, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Marco J Cabrerizo
- Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Illa de Toralla s/n, 36331, Vigo, Spain; Departamento de Ecología y Biología Animal, Universidade de Vigo, Facultad de Ciencias del Mar, Campus Lagoas Marcosende s/n, 36310, Vigo, Spain.
| | - E Walter Helbling
- Estación de Fotobiología Playa Unión, Casilla de Correos 15, 9103, Rawson, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Virginia E Villafañe
- Estación de Fotobiología Playa Unión, Casilla de Correos 15, 9103, Rawson, Chubut, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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11
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Harrison L, Kooienga E, Speights C, Tomberlin J, Lashley M, Barton B, Jordan H. Microbial succession from a subsequent secondary death event following mass mortality. BMC Microbiol 2020; 20:309. [PMID: 33050884 PMCID: PMC7557037 DOI: 10.1186/s12866-020-01969-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/08/2020] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Each death event can be characterized by its associated microbes - a living community of bacteria composed of carcass, soil, and insect-introduced bacterial species - a necrobiome. With the possibility for close succession of these death events, it may be beneficial to characterize how the magnitude of an initial death event may impact the decomposition and necrobiomes of subsequent death events in close proximity. In this paper we hope to characterize the microbial communities associated with a proximate subsequent death event, and distinguish any changes within those communities based on the magnitude of an initial death event and the biomass of preexisting carcass (es) undergoing decomposition. For this experiment, 6 feral swine carcasses in containers were placed in the vicinity of preexisting and ongoing carcass decomposition at sites of three different scales of decomposing carcass biomass. Swab samples were collected from the skin and eye sockets of the container pigs and subjected to 16 s rRNA sequencing and OTU assignment. RESULTS PERMANOVA analysis of the bacterial taxa showed that there was no significant difference in the bacterial communities based on initial mortality event biomass size, but we did see a change in the bacterial communities over time, and slight differences between the skin and ocular cavity communities. Even without soil input, necrobiome communities can change rapidly. Further characterization of the bacterial necrobiome included utilization of the Random Forest algorithm to identify the most important predictors for time of decomposition. Sample sets were also scanned for notable human and swine-associated pathogens. CONCLUSIONS The applications from this study are many, ranging from establishing the environmental impacts of mass mortality events to understanding the importance of scavenger, and scavenger microbial community input on decomposition.
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Affiliation(s)
- Lindsay Harrison
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Emilia Kooienga
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Cori Speights
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Jeffery Tomberlin
- Department of Entomology, Texas A&M University, Minnie Bell Heep Center, Suite 412, College Station, TX, 77843, USA
| | - Marcus Lashley
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Box 9680, Mississippi State, MS, 39762, USA
| | - Brandon Barton
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Heather Jordan
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA.
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12
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Volatile Fatty Acids Production from Microalgae Biomass: Anaerobic Digester Performance and Population Dynamics during Stable Conditions, Starvation, and Process Recovery. Molecules 2019; 24:molecules24244544. [PMID: 31842312 PMCID: PMC6943514 DOI: 10.3390/molecules24244544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/02/2019] [Accepted: 12/10/2019] [Indexed: 11/25/2022] Open
Abstract
Disturbances in anaerobic digestion (AD) negatively impact the overall reactor performance. These adverse effects have been widely investigated for methane generation. However, AD recently appeared as a potential technology to obtain volatile fatty acids (VFAs) and thus, the impact of process disturbances must be evaluated. In this sense, microbial response towards a starvation period of two weeks was investigated resulting in a conversion of organic matter into VFAs of 0.39 ± 0.03 COD-VFAs/CODin. However, the lack of feeding reduced the yield to 0.30 ± 0.02 COD-VFAs/CODin. Microbial analysis revealed that the starvation period favored the syntrophic acetate-oxidizing bacteria coupled with hydrogenotrophic methanogens. Finally, the system was fed at 9 g COD/Ld resulting in process recovery (0.39 ± 0.04 COD-VFAs/CODin). The different microbiome obtained at the end of the process was proved to be functionally redundant, highlighting the AD robustness for VFAs production.
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Zhou J, Song X, Zhang CY, Chen GF, Lao YM, Jin H, Cai ZH. Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea. MICROBIAL ECOLOGY 2018; 76:592-609. [PMID: 29442157 DOI: 10.1007/s00248-018-1150-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
A central goal in marine microecology is to understand the ecological factors shaping spatiotemporal microbial patterns and the underlying processes. We hypothesized that abiotic and/or biotic interactions are probably more important for explaining the distribution patterns of marine bacterioplankton than environmental filtering. In this study, surface seawater samples were collected about 7000 miles from the Mediterranean Sea, transecting the North Atlantic Ocean, to the Brazilian marginal sea. In bacterial biosphere, SAR11, SAR86, Rhodobacteraceae, and Rhodospiriaceae were predominant in the Mediterranean Sea; Prochlorococcus was more frequent in Atlantic Ocean; whereas in the Brazilian coastal sea, the main bacterial members were Synechococcus and SAR11. With respect to archaea, Euryarchaeota were predominant in the Atlantic Ocean and Thaumarchaeota in the Mediterranean Sea. With respect to the eukaryotes, Syndiniales, Spumellaria, Cryomonadida, and Chlorodendrales were predominant in the open ocean, while diatoms and microzooplankton were dominant in the coastal sea. Distinct clusters of prokaryotes and eukaryotes displayed clear spatial heterogeneity. Among the environmental parameters measured, temperature and salinity were key factors controlling bacterial and archaeal community structure, respectively, whereas N/P/Si contributed to eukaryotic variation. The relative contribution of environmental parameters to the microbial distribution pattern was 45.2%. Interaction analysis showed that Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the keystone taxa within the positive-correlation network, while Thermoplasmata was the main contributor in the negative-correlation network. Our study demonstrated that microbial communities are co-governed by environmental filtering and biotic interactions, which are the main deterministic driving factors modulating the spatiotemporal patterns of marine plankton synergistically at the regional or global levels.
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Affiliation(s)
- Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Xiao Song
- The Department of Life Science, Tsinghua University, Beijing, People's Republic of China
| | - Chun-Yun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shangdong Province, People's Republic of China
| | - Guo-Fu Chen
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, Shangdong Province, People's Republic of China.
| | - Yong-Min Lao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Hui Jin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China
| | - Zhong-Hua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen University Town, Room 905, Marine Building, Xili Town, Shenzhen, 518055, Guangdong Province, People's Republic of China.
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14
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Thiem D, Gołębiewski M, Hulisz P, Piernik A, Hrynkiewicz K. How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots? Front Microbiol 2018; 9:651. [PMID: 29720967 PMCID: PMC5915629 DOI: 10.3389/fmicb.2018.00651] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/20/2018] [Indexed: 02/01/2023] Open
Abstract
Black alder (Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall). The dominant type of root microsymbionts of alder were ectomycorrhizal fungi, whose distribution depended on site (salinity): Tomentella, Lactarius, and Phialocephala were more abundant at the saline site. Mortierella and Naucoria (representatives of saprotrophs or endophytes) displayed the opposite tendency. Arbuscular mycorrhizal fungi belonged to Glomeromycota (orders Paraglomales and Glomales), however, they represented less than 1% of all identified fungi. Bacterial community structure depended on test site but not on season. Sequences affiliated with Rhodanobacter, Granulicella, and Sphingomonas dominated at the saline site, while Bradyrhizobium and Rhizobium were more abundant at the non-saline site. Moreover, genus Frankia was observed only at the saline site. In conclusion, bacterial and fungal community structure of alder root microsymbionts and endophytes depends on five soil chemical parameters: salinity, phosphorus, pH, saturation percentage (SP) as well as total organic carbon (TOC), and seasonality does not appear to be an important factor shaping microbial communities. Ectomycorrhizal fungi are the most abundant symbionts of mature alders growing in saline soils. However, specific distribution of nitrogen-fixing Frankia (forming root nodules) and association of arbuscular fungi at early stages of plant development should be taken into account in further studies.
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Affiliation(s)
- Dominika Thiem
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Marcin Gołębiewski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Chair of Plant Physiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Piotr Hulisz
- Department of Soil Science and Landscape Management, Faculty of Earth Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Agnieszka Piernik
- Chair of Geobotany and Landscape Planning, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Toruń, Poland
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15
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Oliveira GHD, Santos-Neto AJ, Zaiat M. Removal of the veterinary antimicrobial sulfamethazine in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor subjected to step changes in the applied organic loading rate. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 204:674-683. [PMID: 28957708 DOI: 10.1016/j.jenvman.2017.09.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/21/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
A bench-scale horizontal-flow anaerobic immobilized biomass (HAIB) reactor treating synthetic swine wastewater was operated under different applied organic loading rates (OLR) through both variations in feed strength and in hydraulic retention time (HRT). The influence of step changes in OLR on the removal of the veterinary antimicrobial sulfamethazine (SMZ) was assessed. The highest observed SMZ removal efficiency, 75 ± 6%, was achieved with an OLR of 2.7 ± 0.4 kg O2 m-3 d-1 when a significant increase in COD removal rate was observed. The SMZ removal rate was positively correlated (r = 0.899) to the COD removal rate in all of the experimental conditions in which the HRT was kept at 24 h, indicating a cometabolic transformation of the antimicrobial. Decreasing the HRT caused a significant decrease in SMZ removal efficiency without affecting the HAIB reactor performance in terms of stability, COD removal or metabolic intermediates production. Functionally equivalent steady states were observed in four different operational phases with similar operating conditions but with widely different behavior in relation to SMZ removal. The experimental results showed the potential of anaerobic technology in removing environmentally relevant concentrations of SMZ, and the possibility of enhancing reactor performance by controlling operating conditions.
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Affiliation(s)
- G H D Oliveira
- Laboratory of Biological Processes, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, 13563-120, São Carlos, São Paulo, Brazil.
| | - A J Santos-Neto
- Institute of Chemistry of São Carlos, University of São Paulo (USP), 400, Trabalhador São-Carlense Ave., 13566-590, São Carlos, São Paulo, Brazil
| | - M Zaiat
- Laboratory of Biological Processes, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, 13563-120, São Carlos, São Paulo, Brazil
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16
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Villasante A, Ramirez C, Catalán N, Romero J. First Report of Swim Bladder-Associated Microbiota in Rainbow Trout (Oncorhynchus mykiss). Microbes Environ 2017; 32:386-389. [PMID: 29033407 PMCID: PMC5745024 DOI: 10.1264/jsme2.me17071] [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] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to identify major bacteria associated with the swim bladder in the rainbow trout, Oncorhynchus mykiss. We extracted DNA from the swim bladder and gut contents in order to perform a temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S rRNA amplicons for bacterial identification to further compare both profiles. Arthrobacter and Cellulosimicrobium were the major genera observed in the swim bladder in fish, but were not present in fish gut contents; Mycoplasma were instead observed in these samples. Further research to investigate the possible symbiotic roles of the swim bladder-associated microbiota in salmonids is needed.
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Affiliation(s)
- Alejandro Villasante
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Carolina Ramirez
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Natalia Catalán
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
| | - Jaime Romero
- Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile Avda
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17
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Pankratov TA, Kachalkin AV, Korchikov ES, Dobrovol’skaya TG. Microbial communities of lichens. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717030134] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Jordan HR, Tomberlin JK. Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains. INSECTS 2017; 8:E54. [PMID: 28538664 PMCID: PMC5492068 DOI: 10.3390/insects8020054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/10/2017] [Accepted: 05/18/2017] [Indexed: 11/17/2022]
Abstract
Abstract: A number of abiotic and biotic factors are known to regulate arthropod attraction, colonization, and utilization of decomposing vertebrate remains. Such information is critical when assessing arthropod evidence associated with said remains in terms of forensic relevance. Interactions are not limited to just between the resource and arthropods. There is another biotic factor that has been historically overlooked; however, with the advent of high-throughput sequencing, and other molecular techniques, the curtain has been pulled back to reveal a microscopic world that is playing a major role with regards to carrion decomposition patterns in association with arthropods. The objective of this publication is to review many of these factors and draw attention to their impact on microbial, specifically bacteria, activity associated with these remains as it is our contention that microbes serve as a primary mechanism regulating associated arthropod behavior.
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Affiliation(s)
- Heather R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39705, USA.
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA.
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19
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Fernandez-Gonzalez N, Huber JA, Vallino JJ. Microbial Communities Are Well Adapted to Disturbances in Energy Input. mSystems 2016; 1:e00117-16. [PMID: 27822558 PMCID: PMC5080406 DOI: 10.1128/msystems.00117-16] [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: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 11/20/2022] Open
Abstract
Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.
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Affiliation(s)
| | - Julie A. Huber
- The Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Joseph J. Vallino
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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20
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McCue MD, Boardman L, Clusella-Trullas S, Kleynhans E, Terblanche JS. The speed and metabolic cost of digesting a blood meal depends on temperature in a major disease vector. ACTA ACUST UNITED AC 2016; 219:1893-902. [PMID: 27059066 DOI: 10.1242/jeb.138669] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/27/2016] [Indexed: 11/20/2022]
Abstract
The energetics of processing a meal is crucial for understanding energy budgets of animals in the wild. Given that digestion and its associated costs may be dependent on environmental conditions, it is necessary to obtain a better understanding of these costs under diverse conditions and identify resulting behavioural or physiological trade-offs. This study examines the speed and metabolic costs - in cumulative, absolute and relative energetic terms - of processing a bloodmeal for a major zoonotic disease vector, the tsetse fly Glossina brevipalpis, across a range of ecologically relevant temperatures (25, 30 and 35°C). Respirometry showed that flies used less energy digesting meals faster at higher temperatures but that their starvation tolerance was reduced, supporting the prediction that warmer temperatures are optimal for bloodmeal digestion while cooler temperatures should be preferred for unfed or post-absorptive flies. (13)C-Breath testing revealed that the flies oxidized dietary glucose and amino acids within the first couple of hours of feeding and overall oxidized more dietary nutrients at the cooler temperatures, supporting the premise that warmer digestion temperatures are preferred because they maximize speed and minimize costs. An independent test of these predictions using a thermal gradient confirmed that recently fed flies selected warmer temperatures and then selected cooler temperatures as they became post-absorptive, presumably to maximize starvation resistance. Collectively these results suggest there are at least two thermal optima in a given population at any time and flies switch dynamically between optima throughout feeding cycles.
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Affiliation(s)
- Marshall D McCue
- Department of Biological Sciences, St Mary's University, San Antonio, TX 78228, USA
| | - Leigh Boardman
- Centre for Invasion Biology, Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Susana Clusella-Trullas
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Elsje Kleynhans
- Centre for Invasion Biology, Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - John S Terblanche
- Centre for Invasion Biology, Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch 7600, South Africa
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21
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Litchman E, Edwards KF, Klausmeier CA. Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future. Front Microbiol 2015; 6:254. [PMID: 25904900 PMCID: PMC4389539 DOI: 10.3389/fmicb.2015.00254] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/15/2015] [Indexed: 11/17/2022] Open
Abstract
Trait-based approaches provide a mechanistic framework to understand and predict the structure and functioning of microbial communities. Resource utilization traits and trade-offs are among key microbial traits that describe population dynamics and competition among microbes. Several important trade-offs have been identified for prokaryotic and eukaryotic microbial taxa that define contrasting ecological strategies and contribute to species coexistence and diversity. The shape, dimensionality, and hierarchy of trade-offs may determine coexistence patterns and need to be better characterized. Laboratory measured resource utilization traits can be used to explain temporal and spatial structure and dynamics of natural microbial communities and predict biogeochemical impacts. Global environmental change can alter microbial community composition through altering resource utilization by different microbes and, consequently, may modify biogeochemical impacts of microbes.
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Affiliation(s)
- Elena Litchman
- W.K. Kellogg Biological Station – Michigan State UniversityHickory Corners, MI, USA
- Department of Integrative Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Kyle F. Edwards
- Department of Oceanography, University of Hawai’i at ManoaHonolulu, HI, USA
| | - Christopher A. Klausmeier
- W.K. Kellogg Biological Station – Michigan State UniversityHickory Corners, MI, USA
- Department of Plant Biology, Michigan State University, East LansingMI, USA
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22
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Wolfe GV, Fitzhugh C, Almasary A, Green A, Bennett P, Wilson M, Siering P. Microbial heterotrophic production in an oligotrophic acidic geothermal lake: responses to organic amendments and terrestrial plant litter. FEMS Microbiol Ecol 2014; 89:606-24. [PMID: 24890617 DOI: 10.1111/1574-6941.12360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/26/2014] [Accepted: 05/21/2014] [Indexed: 02/01/2023] Open
Abstract
Boiling Springs Lake (BSL) is an oligotrophic, acidic geothermal feature where even very low levels of microbial heterotrophic production still exceed autotrophy. To test whether allochthonous leaf litter (LL) inputs fuel this excess, we quantified leaf litterfall, leaching and decomposition kinetics, and measured the impact of organic amendments on production, germination and cell growth, using pyrosequencing to track changes in microbial community composition. Coniferous leaves in BSL exhibited high mass loss rates during leaching and decomposition, likely due to a combination of chemical hydrolysis and contributions of both introduced and endemic microbes. We measured very low in situ (3)H-thymidine incorporation over hours by the dominant chemolithotroph Acidimicrobium (13-65 μg C L(-1) day(-1)), which was inhibited by simple C sources (acetate, glucose). Longer term incubations with additions of 0.01-0.02% complex C/N sources induced germination of the Firmicute Alicyclobacillus within 1-2 days, as well as growth of Acetobacteraceae after 3-4 days. LL additions yielded the opposite successional patterns of these r-selected heterotrophs, boosting production to 30-150 μg C L(-1) day(-1). Growth and germination studies suggest both prokaryotes and fungi likely consume allochthonous organics, and might be novel sources of lignocellulose-degrading enzymes. A model of BSL's C budget supports the hypothesis that allochthonous inputs fuel seasonal microbial heterotrophy, but that dissolved organic C sources greatly exceed direct LL inputs.
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Affiliation(s)
- Gordon V Wolfe
- Department Biological Sciences, California State University, Chico, Chico, CA, USA
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23
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Masrahi A, VandeVoort AR, Arai Y. Effects of silver nanoparticle on soil-nitrification processes. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2014; 66:504-513. [PMID: 24487627 DOI: 10.1007/s00244-013-9994-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/30/2013] [Indexed: 06/03/2023]
Abstract
The release of silver (Ag) nanoparticles (NPs) from the use of consumer products to the environment has raised concern about the risk to ecosystems because of its unpredictable toxicological impact to microorganisms in terrestrial environment. In this study, the impact of Ag chemical speciation (Ag(+) and Ag-NPs [50-nm uncoated and 15-nm polyvinylpyrrolidone (PVP)-coated Ag-NPs]) to soil nitrification kinetics was investigated using a batch soil-slurry nitrification method along with sorption isotherm and dissolution experiments. The results of nitrification potential (i.e., kinetic rate) suggest that Ag(+)/Ag-NPs, which strongly sorb in soils, suppressed the nitrification processes. Among each chemical species, the degree of suppression increased with increasing [Ag]total. Although ionic Ag (Ag(+)) species is known to exhibit greater antimicrobial effects than the solid state Ag species, such as Ag-NPs, in most studies, PVP-coated 15-nm Ag-NPs, however, more effectively suppressed the soil nitrification process than did Ag(+) under the same dose. Although several physicochemical-based toxicity mechanisms of dispersed Ag-NPs were discussed in pure culture and aquatic systems, it is not clearly understood how PVP-coated Ag-NPs could exhibit greater toxicity to nitrifying bacteria than Ag(+) in soils. In assessing the impact of Ag-NPs to microbial mediated processes (e.g., N cycles) in the terrestrial environment, it might be critical to understand the interactions and reactivity of Ag-NPs at the soil-water interface.
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Affiliation(s)
- Abdurrahman Masrahi
- School of Agricultural, Forest and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
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Liang X, Fu Y, Tong L, Liu H. Microbial shifts of the silkworm larval gut in response to lettuce leaf feeding. Appl Microbiol Biotechnol 2014; 98:3769-76. [PMID: 24493569 DOI: 10.1007/s00253-014-5532-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/05/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Silkworm (Bombyx mori L.) larvae were used as an ideal animal protein source for astronauts in the bioregenerative life support system (BLSS). Here, we compared the difference in bacterial communities of the silkworm larval gut between the BLSS rearing way (BRW) and the traditional rearing way (TRW) through culture-dependent approach, 16S rRNA gene analysis, and denaturing gradient gel electrophoresis (DGGE). The culture-dependent approach revealed that the numbers of gut bacteria of silkworm in the BRW significantly decreased compared with that of the TRW. The analysis of clone libraries showed that the gut microbiota in the BRW was significantly less diverse than that in the TRW. Acinetobacter and Bacteroides were dominant populations in the BRW, and Bacillus and Arcobacter dominated in the TRW. DGGE profiles confirmed the difference of silkworm gut bacterial community between two rearing ways. These results demonstrate that gut bacteria change from the BRW contributes to the decrease of silkworm physiological activity. This study increases our understanding of the change of silkworm gut microbiota in response to lettuce leaf feeding in the BRW. We could use the dominant populations to make probiotic products for nutrient absorption and disease prevention in the BLSS to improve gut microecology, as well as the yield and quality of animal protein.
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Affiliation(s)
- Xue Liang
- Laboratory of Environmental Biology and Life Support Technology, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
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Li Y, Fu K, Gao S, Wu Q, Fan L, Li Y, Chen J. Impact on bacterial community in midguts of the Asian corn borer larvae by transgenic Trichoderma strain overexpressing a heterologous chit42 gene with chitin-binding domain. PLoS One 2013; 8:e55555. [PMID: 23457472 PMCID: PMC3574091 DOI: 10.1371/journal.pone.0055555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 12/27/2012] [Indexed: 12/31/2022] Open
Abstract
This paper is the first report of the impact on the bacterial community in the midgut of the Asian corn borer (Ostrinia furnacalis) by the chitinase from the transgenic Trichoderma strain. In this study, we detected a change of the bacterial community in the midgut of the fourth instar larvae by using a culture-independent method. Results suggested that Proteobacteria and Firmicutes were the most highly represented phyla, being present in all the midgut bacterial communities. The observed species richness was simple, ranging from four to five of all the 16S rRNA clone libraries. When using Trichoderma fermentation liquids as additives, the percentages of the dominant flora in the total bacterial community in larval midgut changed significantly. The community of the genus Ochrobactrum in the midgut decreased significantly when the larvae were fed with the fermentation liquids of the transgenic Trichoderma strain Mc4. However, the Enterococcus community increased and then occupied the vacated niche of the Ochrobactrum members. Furthermore, the Shannon-Wiener (H) and the Simpson (1-D) indexes of the larval midgut bacterial library treated by feeding fermentation liquids of the transgenic Trichoderma strain Mc4 was the lowest compared with the culture medium, fermentation liquids of the wild type strain T30, and the sterile artificial diet. The Enterococcus sp. strain was isolated and characterized from the healthy larvae midgut of the Asian corn borer. An infection study of the Asian corn borer larvae using Enterococcus sp. ACB-1 revealed that a correlation existed between the increased Enterococcus community in the larval midgut and larval mortality. These results demonstrated that the transgenic Trichoderma strain could affect the composition of the midgut bacterial community. The change of the midgut bacterial community might be viewed as one of the factors resulting in the increased mortality of the Asian corn borer larvae.
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Affiliation(s)
- Yingying Li
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Kehe Fu
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Shigang Gao
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Qiong Wu
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Lili Fan
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Yaqian Li
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
| | - Jie Chen
- Department of Resource and Environmental Science, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, China
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Cabrol L, Malhautier L, Poly F, Lepeuple AS, Fanlo JL. Bacterial dynamics in steady-state biofilters: beyond functional stability. FEMS Microbiol Ecol 2012; 79:260-71. [PMID: 22029727 DOI: 10.1111/j.1574-6941.2011.01213.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.
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Affiliation(s)
- Léa Cabrol
- Veolia Environnement Recherche et Innovation, Maisons Laffitte, France
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Integrating microbial ecology in bioprocess understanding: the case of gas biofiltration. Appl Microbiol Biotechnol 2011; 90:837-49. [PMID: 21424795 DOI: 10.1007/s00253-011-3191-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 02/25/2011] [Accepted: 02/27/2011] [Indexed: 10/18/2022]
Abstract
Biofilters are packed-bed bioreactors where contaminants, once transferred from the gas phase to the biofilm, are oxidized by diverse and complex communities of attached microorganisms. Over the last decade, more and more studies aimed at opening the back box of biofiltration by unraveling the biodiversity-ecosystem function relationship. In this review, we report the insights provided by the microbial ecology approach in biofilters and we emphasize the parallels existing with other engineered ecosystems used for wastewater treatment, as they all constitute relevant model ecosystems to explore ecological issues. We considered three characteristic ecological indicators: the density, the diversity, and the structure of the microbial community. Special attention was paid to the temporal and spatial dynamics of each indicator, insofar as it can disclose the potential relationship, or absence of relation, with any operating or functional parameter. We also focused on the impact of disturbance regime on the microbial community structure, in terms of resistance, resilience, and memory. This literature review led to mitigated conclusions in terms of biodiversity-ecosystem function relationship. Depending on the environmental system itself and the way it is investigated, the spatial and temporal dynamics of the microbial community can be either correlated (e.g., spatial stratification) or uncoupled (e.g., temporal instability) to the ecosystem function. This lack of generality shows the limits of current 16S approach in complex ecosystems, where a functional approach may be more suitable.
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Ji G, Tong J, Tan Y. Wastewater treatment efficiency of a multi-media biological aerated filter (MBAF) containing clinoptilolite and bioceramsite in a brick-wall embedded design. BIORESOURCE TECHNOLOGY 2011; 102:550-557. [PMID: 20797854 DOI: 10.1016/j.biortech.2010.07.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 07/12/2010] [Accepted: 07/18/2010] [Indexed: 05/29/2023]
Abstract
A multi-media biological aerated filter (MBAF) with clinoptilolite media was used to treat synthetic wastewater. Coal ash bioceramsite with supplemental metallic iron was added to the clinoptilolite media of MBAFs in a brick-wall embedded design. Performance parameters, such as hydraulic, organic, N and P loading capacity and microbial community composition were studied for different quantity of supplemental metallic iron contained in three MBAFs. The MBAFs with more metallic iron were found to have superior hydraulic and organic loading, and higher N and P capacities. COD, NH3-N and TP removal dropped by 7-10%, 6-7% and 4-5%, respectively, with when hydraulic loading was raised from 2.8 to 7.5 m3 m(-2) d(-1). NH3-N removal also decreased 8-9% when ammonia loading was elevated from 0.078 to 0.156 kg NH3-N m(-3) d(-1). Real-time PCR revealed a relatively stable bacterial community composed primarily of eubacteria that formed after an initial 120 d operational period. Doubling the amount of metallic iron in the bioceramsite media resulted in a twofold increase of eubacteria in the MBAF, but a decrease in the ratio of anaerobic ammonia-oxidizing bacteria to total bacteria.
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Affiliation(s)
- Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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Li M, Lee SK, Yang SH, Ko JH, Han JS, Kim TJ, Suh JW. ATP modulates the growth of specific microbial strains. Curr Microbiol 2010; 62:84-9. [PMID: 20512647 DOI: 10.1007/s00284-010-9677-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 05/07/2010] [Indexed: 11/28/2022]
Abstract
The regulatory function of extracellular ATP (exATP) in bacteria is unknown, but recent studies have demonstrated exATP induced enhanced secondary metabolite production and morphological differentiation in Streptomyces coelicolor. The growth of Streptomyces coelicolor, however, was unaffected by exATP, although changes in growth are common phenotypes. To identify bacteria whose growth is altered by exATP, we measured exATP-induced population changes in fast-growing microbes and actinomycetes in compost. Compared with the water-treated control, the addition of 10 ml 100 μM ATP to 10 g of compost enhanced the actinomycetes population by 30% and decreased fast-growing microbial numbers by 20%. Eight microbes from each group were selected from the most populated colony, based on appearance. Of the eight isolated fast-growing microbes, the 16S rRNA sequences of three isolates were similar to the plant pathogens Serratia proteamaculans and Sphingomonas melonis, and one was close to a human pathogen, Elizabethkingia meningoseptica. The growth of all fast-growing microbes was inhibited by ATP, which was confirmed in Pseudomonas syringae DC3000, a pathogenic plant bacterium. The growth of six of eight isolated actinomycetes strains, all of which were identified as close to Streptomyces neyagawaensis, was enhanced by ATP treatment. This study suggests that exATP regulates bacterial physiology and that the exATP response system is a target for the control of bacterial ecology.
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Affiliation(s)
- Ming Li
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 449-728, South Korea
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Marzorati M, Balloi A, de Ferra F, Corallo L, Carpani G, Wittebolle L, Verstraete W, Daffonchio D. Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer. Microb Cell Fact 2010; 9:12. [PMID: 20170484 PMCID: PMC2834577 DOI: 10.1186/1475-2859-9-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 02/19/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ. RESULTS We report the characterization of the response of an enriched bacterial community of a 1,2-dichloroethane (1,2-DCA) contaminated aquifer to the spiking with 5 mM lactate as electron donor in microcosm studies. After 15 days of incubation, the microbial community structure was analyzed. The bacterial 16S rRNA gene clone library showed that the most represented phylogenetic group within the consortium was affiliated with the phylum Firmicutes. Among them, known degraders of chlorinated compounds were identified. A reductive dehalogenase genes clone library showed that the community held four phylogenetically-distinct catalytic enzymes, all conserving signature residues previously shown to be linked to 1,2-DCA dehalogenation. CONCLUSIONS The overall data indicate that the enriched bacterial consortium shares the metabolic functionality between different members of the microbial community and is characterized by a high functional redundancy. These are fundamental features for the maintenance of the community's functionality, especially under stress conditions and suggest the feasibility of a bioremediation treatment with a potential prompt dehalogenation and a process stability over time.
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Affiliation(s)
- Massimo Marzorati
- DISTAM, Dipartimento di Scienze e Tecnologie alimentari e Microbiologiche, Università degli Studi di Milano, 20133 Milan, Italy
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Robinson CJ, Schloss P, Ramos Y, Raffa K, Handelsman J. Robustness of the bacterial community in the cabbage white butterfly larval midgut. MICROBIAL ECOLOGY 2010; 59:199-211. [PMID: 19924467 PMCID: PMC2836246 DOI: 10.1007/s00248-009-9595-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 09/16/2009] [Indexed: 05/03/2023]
Abstract
Microbial communities typically vary in composition and structure over space and time. Little is known about the inherent characteristics of communities that govern various drivers of these changes, such as random variation, changes in response to perturbation, or susceptibility to invasion. In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of community structure on susceptibility to invasion. We compared communities in larvae experiencing the same conditions at different times (temporal variation) or fed different diets (perturbation). The most highly represented phylum was Proteobacteria, which was present in all midgut communities. The observed species richness ranged from six to 15, and the most abundant members affiliated with the genera Methylobacteria, Asaia, Acinetobacter, Enterobacter, and Pantoea. Individual larvae subjected to the same conditions at the same time harbored communities that were highly similar in structure and membership, whereas the communities observed within larval populations changed with diet and over time. In addition, structural changes due to perturbation coincided with enhanced susceptibility to invasion by Enterobacter sp. NAB3R and Pantoea stewartii CWB600, suggesting that resistance to invasion is in part governed by community structure. These findings along with the observed conservation of membership at the phylum level, variation in structure and membership at lower taxonomic levels, and its relative simplicity make the cabbage white butterfly larval community an attractive model for studying community dynamics and robustness.
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Affiliation(s)
- Courtney J. Robinson
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: Departments of Internal Medicine and Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48104 USA
| | - Patrick Schloss
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Present Address: University of Michigan, Department of Microbiology & Immunology, Ann Arbor, 48109 MI USA
| | - Yolied Ramos
- Department of Industrial Microbiology, University of Puerto Rico-Mayagüez, Mayagüez, PR 00681 USA
| | - Kenneth Raffa
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Jo Handelsman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706 USA
- 1550 Linden Drive, Madison, WI 53706 USA
- University of Wisconsin-Madison, Madison, WI 53706 USA
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Longnecker K, Da Costa A, Bhatia M, Kujawinski EB. Effect of carbon addition and predation on acetate-assimilating bacterial cells in groundwater. FEMS Microbiol Ecol 2009; 70:456-70. [DOI: 10.1111/j.1574-6941.2009.00767.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Han C, Spring S, Lapidus A, Del Rio TG, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Saunders E, Chertkov O, Brettin T, Göker M, Rohde M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Detter JC. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). Stand Genomic Sci 2009; 1:54-62. [PMID: 21304637 PMCID: PMC3035210 DOI: 10.4056/sigs.22138] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum ‘Bacteroidetes’. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Ponnusamy L, Xu N, Stav G, Wesson DM, Schal C, Apperson CS. Diversity of bacterial communities in container habitats of mosquitoes. MICROBIAL ECOLOGY 2008; 56:593-603. [PMID: 18373113 PMCID: PMC2904961 DOI: 10.1007/s00248-008-9379-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 02/16/2008] [Indexed: 05/19/2023]
Abstract
We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n = 12), cemetery urns (n = 23), and miscellaneous containers that included two tree holes (n = 19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species.
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Affiliation(s)
- Loganathan Ponnusamy
- Department of Entomology, North Carolina State University, Campus Box 7647, Raleigh, NC 27695-7647, USA
| | - Ning Xu
- Department of Entomology, North Carolina State University, Campus Box 7647, Raleigh, NC 27695-7647, USA
| | - Gil Stav
- Department of Tropical Medicine, Tulane Health Sciences Center, Tulane University, New Orleans, LA 70112, USA
| | - Dawn M. Wesson
- Department of Tropical Medicine, Tulane Health Sciences Center, Tulane University, New Orleans, LA 70112, USA
| | - Coby Schal
- Department of Entomology, North Carolina State University, Campus Box 7647, Raleigh, NC 27695-7647, USA
| | - Charles S. Apperson
- Department of Entomology, North Carolina State University, Campus Box 7647, Raleigh, NC 27695-7647, USA
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Abstract
The rate, timing, and quality of resource supply exert strong controls on a wide range of ecological processes. In particular, resource-mediated changes in microbial activity have the potential to alter ecosystem processes, including the production and respiration of organic matter. In this study, we used field experiments and simulation modeling to explore how aquatic heterotrophic bacteria respond to variation in resource quality (low vs. high) and resource schedule (pulse vs. press). Field experiments revealed that one-time pulse additions of resources in the form of dissolved organic carbon (DOC) caused short-lived (< or =48 h) peaks in bacterial productivity (BP), which translated into large differences across treatments: cumulative BP was twice as high in the pulse vs. press treatment under low resource quality, and five times as high under high resource quality. To gain a more mechanistic understanding of microbial productivity in variable resource environments, we constructed a mathematical model to explore the attributes of bacterial physiology and DOC supply that might explain the patterns observed in our field experiments. Model results suggest that the mobilization rate of refractory to labile carbon, an index of resource quality, was critical in determining cumulative differences in BP between pulse and press resource environments (BPPu:Pr ratios). Moreover, BPPu:Pr ratios were substantially larger when our model allowed for realistic changes in bacterial growth efficiency as a function of bacterial carbon consumption. Together, our field and modeling results imply that resource schedule is important in determining the flow of material and energy from microbes to higher trophic levels in aquatic food webs, and that the effects of resource quality are conditional upon resource schedule. An improved understanding of the effects of resource variability on microorganisms is therefore critical for predicting potential changes in ecosystem functioning in response to environmental change, such as altered DOC fluxes from terrestrial to aquatic ecosystems.
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Affiliation(s)
- Jay T Lennon
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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Diversity of cutaneous bacteria with antifungal activity isolated from female four-toed salamanders. ISME JOURNAL 2007; 2:145-57. [DOI: 10.1038/ismej.2007.110] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Impact of non-ionic surfactant on the long-term development of lab-scale-activated sludge bacterial communities. Res Microbiol 2007; 158:712-7. [PMID: 18054204 DOI: 10.1016/j.resmic.2007.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 09/14/2007] [Accepted: 09/21/2007] [Indexed: 11/23/2022]
Abstract
The development of bacterial communities in replicate lab-scale-activated sludge reactors degrading a non-ionic surfactant was evaluated by statistical analysis of denaturing gradient gel electrophoresis (DGGE) fingerprints. Four sequential batch reactors were fed with synthetic sewage, two of which received, in addition, 0.01% of nonylphenol ethoxylates (NPE). The dynamic character of bacterial community structure was confirmed by the differences in species composition among replicate reactors. Measurement of similarities between reactors was obtained by pairwise similarity analysis using the Bray Curtis coefficient. The group of NPE-amended reactors exhibited the highest similarity values (Sjk=0.53+/-0.03), indicating that the bacterial community structure of NPE-amended reactors was better replicated than control reactors (Sjk=0.36+/-0.04). Replicate NPE-amended reactors taken at different times of operation clustered together, whereas analogous relations within the control reactor cluster were not observed. The DGGE pattern of isolates grown in conditioned media prepared with media taken at the end of the aeration cycle grouped separately from other conditioned and synthetic media regardless of the carbon source amendment, suggesting that NPE degradation residuals could have a role in the shaping of the community structure.
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Bittner AC, Croffut RM, Stranahan MC, Yokelson TN. Prescript-assist probiotic-prebiotic treatment for irritable bowel syndrome: an open-label, partially controlled, 1-year extension of a previously published controlled clinical trial. Clin Ther 2007; 29:1153-60. [PMID: 17692729 DOI: 10.1016/j.clinthera.2007.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2007] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study was to extend a previous 2-week assessment of a probiotic-prebiotic complex in patients with irritable bowel syndrome (IBS). METHODS In this open-label, partially controlled, 1-year (14 [2] months) extension study, data were collected from patients with IBS who continued treatment following a 2-week study of the efficacy of the probiotic-prebiotic complex. Data were collected at 2 and approximately 60 weeks after the end of the original study. RESULTS A total of 25 patients entered the 2-week extension and 22 completed the approximately 60-week follow-up study (20 women, 2 men; age range, 20-70 years; all white). Results in the control group 2 weeks after crossover to treatment were similar to those from the original study, with reductions in IBS subsyndromes, as follows: general ill feelings/nausea (P < 0.001), indigestion/flatulence (P < 0.001), and marginally colitis (P < 0.03 [1-tailed]). Treatment was associated with a continued reduction in general ill feelings/nausea at 4 weeks (P < 0.007). At >or=52-week follow-up, the rate of remissions was 81.5% to 100% (P < 0.003). CONCLUSION Based on the results from the present 1-year extension study, treatment with this probiotic-prebiotic complex may be an option for short-term (2-4 weeks) and long-term ( approximately 60-week) reductions in IBS symptoms.
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Konopka A, Carrero-Colon M, Nakatsu CH. Community dynamics and heterogeneities in mixed bacterial communities subjected to nutrient periodicities. Environ Microbiol 2007; 9:1584-90. [PMID: 17504495 DOI: 10.1111/j.1462-2920.2007.01326.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sixteen replicate microcosms were inoculated with a mixed assemblage of heterotrophic bacteria and provided with discrete pulses of protein as carbon and energy source. The dynamics of community structure were monitored by 16S rRNA gene polymerase chain reaction denaturant gradient gel electrophoresis (PCR-DGGE). The results were consistent with a strong role for biological interactions in maintaining diversity. Replicate microcosms developed different microbial communities. For systems exposed to nutrient pulses every 7 days, the number of DGGE bands averaged 13 +/- 4 (mean +/- SD) and the Dice similarity coefficient between pairs ranged from 0.08 to 0.67. In each of 16 systems provided protein once each day, there were dynamic changes over the first 30 days but community composition was stable over the next 20 days. However, most systems differed from each other; two-thirds of the pairwise comparisons had similarity coefficients in the range of 0.35-0.63. These 16 systems contained 10 +/- 2 phylotypes (mean +/- SD) and in aggregate 34 phylotypes were found in the 16 systems. Most phylotypes were found in < 25% of the systems, and there were not strong networks of association among phylotypes.
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Affiliation(s)
- Allan Konopka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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