151
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Scott JT, Cotner JB, Lapara TM. Variable stoichiometry and homeostatic regulation of bacterial biomass elemental composition. Front Microbiol 2012; 3:42. [PMID: 22371708 PMCID: PMC3283892 DOI: 10.3389/fmicb.2012.00042] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/26/2012] [Indexed: 11/20/2022] Open
Abstract
Prokaryotic heterotrophs (hereafter, bacteria) represent a large proportion of global biomass, and therefore bacterial biomass stoichiometry likely exerts control on global phosphorus (P), carbon (C), and nitrogen cycling and primary productivity. In this study we grew recently isolated freshwater heterotrophic bacteria across an ecologically relevant range of resource C:P ratios (organic C to P ratio in available resources) to quantify the P requirements of these organisms and examine the degree to which they regulated their P content under P-sufficient and P-deficient conditions. Bacterial biomass was only limited by P when resource C:P was greater than 250 (by atoms). Bacterial C:P ranged from 71 to 174 under P sufficiency and from 252 to 548 under P deficiency. Bacteria exhibited very little C:P homeostasis under P-sufficient growth conditions, greater C:P homeostasis under P-deficient conditions, and the ability of bacteria to outcompete one another in short-term experiments depended on a tradeoff between storing excess P for later use under P-deficient conditions or immediately using P to produce more biomass. These results indicate that freshwater heterotrophic bacteria are not as P-rich as previously thought and that homeostatic regulation of C:P stoichiometry depends on the individual taxa and what resource (organic C or available P) is limiting bacterial growth. Individual bacterial populations can vary between strong C:P homeostasis under P deficiency to virtually no C:P homeostasis under P sufficiency, but variation between taxa and the effect this has on competitive ability may dampen the signal in C:PB at the bacterial community level. Nevertheless, the prevalence of homeostatic and non-homeostatic strategies in a bacterial community should have important implications for nutrient regeneration and carbon cycling.
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Affiliation(s)
- J Thad Scott
- Department of Ecology, Evolution, and Behavior, University of Minnesota St. Paul, MN, USA
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152
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Abed RM, Ramette A, Hübner V, Deckker P, Beer D. Microbial diversity of eolian dust sources from saline lake sediments and biological soil crusts in arid Southern Australia. FEMS Microbiol Ecol 2012; 80:294-304. [DOI: 10.1111/j.1574-6941.2011.01289.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 11/11/2011] [Accepted: 12/22/2011] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - Alban Ramette
- Max-Planck Institute for Marine Microbiology; Bremen; Germany
| | - Vera Hübner
- Max-Planck Institute for Marine Microbiology; Bremen; Germany
| | - Patrick Deckker
- Research School of Earth Sciences; The Australian National University; Canberra; Australia
| | - Dirk Beer
- Max-Planck Institute for Marine Microbiology; Bremen; Germany
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153
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Unexpected stability of Bacteroidetes and Firmicutes communities in laboratory biogas reactors fed with different defined substrates. Appl Environ Microbiol 2012; 78:2106-19. [PMID: 22247168 DOI: 10.1128/aem.06394-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the present study, bacterial communities in 200-liter biogas reactors containing liquid manure consecutively fed with casein, starch, and cream were investigated over a period of up to 33 days. A 16S rRNA gene clone library identified Bacteroidetes and Firmicutes as the most abundant bacterial groups in the starting material, at 58.9% and 30.1% of sequences, respectively. The community development of both groups was monitored by real-time PCR and single-strand conformation polymorphism (SSCP) analysis. The Firmicutes and Bacteroidetes communities were unexpectedly stable and hardly influenced by batch-feeding events. The continuous feeding of starch led to community shifts that nevertheless contributed to a stable reactor performance. A longer starving period and a change in the pH value resulted in further community shifts within the Bacteroidetes but did not influence the Firmicutes. Predominant DNA bands from SSCP gels were cloned and sequenced. Sequences related to Peptococcaceae, Cytophagales, and Petrimonas sulfuriphila were found in all samples from all experiments. Real-time PCR demonstrated the abundance of members of the phylum Bacteroidetes and also reflected changes in gene copy numbers in conjunction with a changing pH value and acetate accumulation.
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154
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Lee SH, Kang HJ, Lee YH, Lee TJ, Han K, Choi Y, Park HD. Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters. ACTA ACUST UNITED AC 2012; 14:1893-905. [DOI: 10.1039/c2em10958a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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155
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Wells GF, Park HD, Eggleston B, Francis CA, Criddle CS. Fine-scale bacterial community dynamics and the taxa-time relationship within a full-scale activated sludge bioreactor. WATER RESEARCH 2011; 45:5476-5488. [PMID: 21875739 DOI: 10.1016/j.watres.2011.08.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 07/18/2011] [Accepted: 08/06/2011] [Indexed: 05/31/2023]
Abstract
In activated sludge bioreactors, aerobic heterotrophic communities efficiently remove organics, nutrients, toxic substances, and pathogens from wastewater, but the dynamics of these communities are as yet poorly understood. A macroecology metric used to quantify community shifts is the taxa-time relationship, a temporal analog of the species-area curve. To determine whether this metric can be applied to full-scale bioreactors, activated sludge samples were collected weekly over a one-year period at a local municipal wastewater treatment plant. Bacterial community dynamics were evaluated by monitoring 16S rRNA genes using Terminal Restriction Fragment Length Polymorphism (T-RFLP), corroborated by clone libraries. Observed taxa richness increased with time according to a power law model, as predicted by macroecological theory, with a power law exponent of w = 0.209. The results reveal strong long-term temporal dynamics during a period of stable performance (BOD removal and nitrification). Community dynamics followed a gradual succession away from initial conditions rather than periodicity around a mean "equilibrium", with greater within-month then among-month community similarities. Changes in community structure were significantly associated via multivariate statistical analyses with dissolved oxygen, temperature, influent silver, biomass (MLSS), flow rate, and influent nitrite, cadmium and chromium concentrations. Overall, our results suggest patterns of bacterial community dynamics likely regulated in part by operational parameters and provide evidence that the taxa-time relationship may be a fundamental ecological pattern in macro- and microbial systems.
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Affiliation(s)
- George F Wells
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
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156
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Monteils V, Rey M, Cauquil L, Troegeler-Meynadier A, Silberberg M, Combes S. Random changes in the heifer rumen in bacterial community structure, physico-chemical and fermentation parameters, and in vitro fiber degradation. Livest Sci 2011. [DOI: 10.1016/j.livsci.2011.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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157
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Anaerobic digestibility of marine microalgae Phaeodactylum tricornutum in a lab-scale anaerobic membrane bioreactor. Appl Microbiol Biotechnol 2011; 93:859-69. [DOI: 10.1007/s00253-011-3624-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 09/12/2011] [Accepted: 09/30/2011] [Indexed: 11/26/2022]
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158
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Comte J, Del Giorgio PA. Composition influences the pathway but not the outcome of the metabolic response of bacterioplankton to resource shifts. PLoS One 2011; 6:e25266. [PMID: 21980410 PMCID: PMC3181318 DOI: 10.1371/journal.pone.0025266] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 08/30/2011] [Indexed: 11/19/2022] Open
Abstract
Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations.
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Affiliation(s)
- Jérôme Comte
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada.
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159
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Xu S, Liu H. New exoelectrogen Citrobacter sp. SX-1 isolated from a microbial fuel cell. J Appl Microbiol 2011; 111:1108-15. [DOI: 10.1111/j.1365-2672.2011.05129.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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160
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Yang C, Zhang W, Liu R, Li Q, Li B, Wang S, Song C, Qiao C, Mulchandani A. Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:7408-7415. [PMID: 21780771 DOI: 10.1021/es2010545] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The activated sludge process is an essential process for treating domestic and industrial wastewaters in most wastewater treatment plants (WWTPs). This process consists of a mixture of general and special microorganisms in a form of a complex enrichment population. Thus, the exploration of activated sludge microbial communities is crucial to improve the performance of activated sludge process. In this study, we investigated the phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale WWTPs. Four 16S rRNA gene clone libraries were constructed from activated sludge samples. In all samples, Proteobacteria was the most abundant phylogenetic group, followed by Bacteroidetes and Firmicutes. The dominance of Proteobacteria was further demonstrated by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP). Some specific genera, e.g., Nitrosomonas, Thauera, and Dechloromonas, which significantly correlate with the functions and performance of wastewater treatment, were abundant in all samples. A large number of unclassified sequences were found in the library, suggesting that a wide variety of novel species may inhabit complex activated sludge communities. The structures of the bacterial community did not differ significantly among samples. All samples utilized the vast majority of 31 carbon sources of an EcoPlate (Biolog), suggesting that activated sludge microbial communities possess high metabolic potential and equivalent functions required for wastewater treatment.
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Affiliation(s)
- Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai University, Tianjin 300071, China
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161
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Oz NA, Ince O, Turker G, Ince BK. Effect of seed sludge microbial community and activity on the performance of anaerobic reactors during the start-up period. World J Microbiol Biotechnol 2011; 28:637-47. [DOI: 10.1007/s11274-011-0857-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 08/02/2011] [Indexed: 11/30/2022]
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162
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Acharya BK, Pathak H, Mohana S, Shouche Y, Singh V, Madamwar D. Kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash. WATER RESEARCH 2011; 45:4248-4259. [PMID: 21704352 DOI: 10.1016/j.watres.2011.05.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 05/14/2011] [Accepted: 05/31/2011] [Indexed: 05/31/2023]
Abstract
Anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. Treatment efficiency of the bioreactor was investigated at different hydraulic retention times (HRT) and organic loading rates (OLR 5-20 kg COD m⁻³ d⁻¹). Applying the modified Stover-Kincannon model to the reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 2 kg m⁻³ d⁻¹ and 1.69 kg m⁻³ d⁻¹ respectively. Bacterial community structures of acidogenic and methanogenic reactors were assessed using culture-independent analyses. Sequencing of 16S rRNA genes exhibited a total of 123 distinct operational taxonomic units (OTUs) comprising 49 from acidogenic reactor and 74 (28 of eubacteria and 46 of archaea) from methanogenic reactor. The findings reveal the role of Lactobacillus sp. (Firmicutes) as dominant acid producing organisms in acidogenic reactor and Methanoculleus sp. (Euryarchaeotes) as foremost methanogens in methanogenic reactor.
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Affiliation(s)
- Bhavik K Acharya
- BRD School of Bioscience, Sardar Patel Maidan, Vadtal Road, Satellite Campus, PO Box 39, Sardar Patel University, Vallabh Vidyanagar 388120, Gujarat, India
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163
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Tang YQ, Ji P, Hayashi J, Koike Y, Wu XL, Kida K. Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding. Appl Microbiol Biotechnol 2011; 91:1447-61. [DOI: 10.1007/s00253-011-3479-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 06/28/2011] [Accepted: 07/13/2011] [Indexed: 11/28/2022]
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164
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Ecosystems biology of microbial metabolism. Curr Opin Biotechnol 2011; 22:541-6. [PMID: 21592777 DOI: 10.1016/j.copbio.2011.04.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 03/31/2011] [Accepted: 04/20/2011] [Indexed: 11/22/2022]
Abstract
The metabolic capabilities of many environmentally and medically important microbes can be quantitatively explored using systems biology approaches to metabolic networks. Yet, as we learn more about the complex microbe-microbe and microbe-environment interactions in microbial communities, it is important to understand whether and how system-level approaches can be extended to the ecosystem level. Here we summarize recent work that addresses these challenges at multiple scales, starting from two-species natural and synthetic ecology models, up to biosphere-level approaches. Among the many fascinating open challenges in this field is whether the integration of high throughput sequencing methods and mathematical models will help us capture emerging principles of ecosystem-level metabolic organization and evolution.
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165
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Abstract
Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis.
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Affiliation(s)
- Mitch D Day
- Mitch D. Day ( ) is a postdoctoral fellow, Daniel Beck is a doctoral student, and James A. Foster is a professor, all in the Department of Biological Sciences at the University of Idaho, in Moscow, Idaho. All are affiliated with the Initiative for Bioinformatics and Evolutionary Studies (IBEST), an interdisciplinary center devoted to developing a greater understanding of the patterns and processes of evolution and their relevance to biomedicine. All are also members of the National Science Foundation Science and Technology Center, BEACON, for the study of evolution in action
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166
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Variations in methanogenic population structure under overloading of pre-acidified high-strength organic wastewaters. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.01.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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167
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Ayarza JM, Erijman L. Balance of neutral and deterministic components in the dynamics of activated sludge floc assembly. MICROBIAL ECOLOGY 2011; 61:486-95. [PMID: 20972561 DOI: 10.1007/s00248-010-9762-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 10/10/2010] [Indexed: 05/20/2023]
Abstract
Understanding the processes that generate patterns of community structure is a central focus of ecological research. With that aim, we manipulated the structure of bacterial activated sludge to test the influence of the species richness and composition of bacterial communities on the dynamics of activated sludge floc assembly in lab-scale bioreactors. Bacterial community structure was analyzed using denaturing gradient gel electrophoresis of RT-PCR amplified 16S rRNA. Fingerprinting of four parallel reactors, started with the same source communities added in different proportions, converged to patterns that were more similar than expected by chance, suggesting a deterministic selection in floc development. Evidence for neutral dynamics was suggested by the dependence of the rate of replacement of species (bacterial taxa-time relationships) on the number of available species in the source community. Further indication of stochastic dynamics was obtained by the application of the Sloan neutral model for prokaryotes. The fitting of the observed data to the model predictions revealed that the importance of the stochastic component increased with the size of the reservoir of species richness from which the community is drawn. Taken together, the results illustrate how both neutral and deterministic dynamics operate simultaneously in the assembly of the bacterial floc and show that the balance of the two depends on the richness of the source community.
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Affiliation(s)
- Joaquín M Ayarza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
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168
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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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169
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Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 2011; 75:14-49. [PMID: 21372319 PMCID: PMC3063352 DOI: 10.1128/mmbr.00028-10] [Citation(s) in RCA: 844] [Impact Index Per Article: 64.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stuart E. Jones
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Alexander Eiler
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Katherine D. McMahon
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stefan Bertilsson
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
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170
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Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A 2011; 108:4158-63. [PMID: 21368115 DOI: 10.1073/pnas.1015676108] [Citation(s) in RCA: 289] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated the relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment (i.e., operating conditions) in a yearlong monthly time series of nine full-scale bioreactor facilities treating brewery wastewater (>20,000 measurements). Each of the nine facilities had a unique community structure with an unprecedented level of stability. Using machine learning, we identified a small subset of operational taxonomic units (OTUs; 145 out of 4,962), which predicted the location of the facility of origin for almost every sample (96.4% accuracy). Of these 145 OTUs, syntrophic bacteria were systematically overrepresented, demonstrating that syntrophs rebounded following disturbances. This indicates that resilience, rather than dynamic competition, played an important role in maintaining the necessary syntrophic populations. In addition, we explained the observed phylogenetic differences between all samples on the basis of a subset of environmental gradients (using constrained ordination) and found stronger relationships between community structure and its function rather than its environment. These relationships were strongest for two performance variables--methanogenic activity and substrate removal efficiency--both of which were also affected by microbial ecology because these variables were correlated with community evenness (at any given time) and variability in phylogenetic structure (over time), respectively. Thus, we quantified relationships between community structure and function, which opens the door to engineer communities with superior functions.
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171
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Wang X, Wen X, Yan H, Ding K, Zhao F, Hu M. Bacterial community dynamics in a functionally stable pilot-scale wastewater treatment plant. BIORESOURCE TECHNOLOGY 2011; 102:2352-7. [PMID: 21095118 DOI: 10.1016/j.biortech.2010.10.095] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/17/2010] [Accepted: 10/20/2010] [Indexed: 05/07/2023]
Abstract
To determine whether functional stability was correlated with a stable microbial community structure in a functionally stable pilot-scale wastewater treatment plant, bacterial communities in the system were monitored over a one-year period. Bacterial community dynamics was characterized by the terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. During the study period, the effluent BOD concentrations were very stable, with the average BOD concentration below 10 mg/L. The effluent TN concentrations were always below 20 mg/L, except for the first 40 days. T-RFLP results showed that, during the test period, the bacterial community structures were not stable, with an average change rate (every 15 days) of 20.4%±11.2%. Based on Lorenz distribution curves, it was observed that 20% of the species corresponded with 40-77% of cumulative relative abundances. Results clearly revealed that, in the pilot-scale wastewater treatment plant, functional stability did not correlate with stable bacterial communities.
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Affiliation(s)
- Xiaohui Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, Department of Environmental Science and Engineering, Tsinghua University, Beijing, PR China
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172
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Wan CY, De Wever H, Diels L, Thoeye C, Liang JB, Huang LN. Biodiversity and population dynamics of microorganisms in a full-scale membrane bioreactor for municipal wastewater treatment. WATER RESEARCH 2011; 45:1129-1138. [PMID: 21112606 DOI: 10.1016/j.watres.2010.11.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2010] [Revised: 09/30/2010] [Accepted: 11/04/2010] [Indexed: 05/27/2023]
Abstract
The total, ammonia-oxidizing, and denitrifying Bacteria in a full-scale membrane bioreactor (MBR) were evaluated monthly for over one year. Microbial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the 16S rRNA and ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes. The community fingerprints obtained were compared to those from a conventional activated sludge (CAS) process running in parallel treating the same domestic wastewater. Distinct DGGE profiles for all three molecular markers were observed between the two treatment systems, indicating the selection of specific bacterial populations by the contrasting environmental and operational conditions. Comparative 16S rRNA sequencing indicated a diverse bacterial community in the MBR, with phylotypes from the α- and β-Proteobacteria and Bacteroidetes dominating the gene library. The vast majority of sequences retrieved were not closely related to classified organisms or displayed relatively low levels of similarity with any known 16S rRNA gene sequences and thus represent organisms that constitute new taxa. Similarly, the majority of the recovered nosZ sequences were novel and only moderately related to known denitrifiers from the α- and β-Proteobacteria. In contrast, analysis of the amoA gene showed a remarkably simple ammonia-oxidizing community with the detected members almost exclusively affiliated with the Nitrosomonas oligotropha lineage. Major shifts in total bacteria and denitrifying community were detected and these were associated with change in the external carbon added for denitrification enhancement. In spite of this, the MBR was able to maintain a stable process performance during that period. These results significantly expand our knowledge of the biodiversity and population dynamics of microorganisms in MBRs for wastewater treatment.
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Affiliation(s)
- Cai-Yun Wan
- Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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173
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Current knowledge of microbial community structures in landfills and its cover soils. Appl Microbiol Biotechnol 2010; 89:961-9. [DOI: 10.1007/s00253-010-3024-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 11/17/2010] [Accepted: 11/17/2010] [Indexed: 10/18/2022]
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174
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Wang X, Wen X, Yan H, Ding K, Hu M. Community dynamics of ammonia oxidizing bacteria in a full-scale wastewater treatment system with nitrification stability. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s11783-010-0254-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
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175
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Dohrmann AB, Baumert S, Klingebiel L, Weiland P, Tebbe CC. Bacterial community structure in experimental methanogenic bioreactors and search for pathogenic clostridia as community members. Appl Microbiol Biotechnol 2010; 89:1991-2004. [DOI: 10.1007/s00253-010-2955-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/12/2010] [Accepted: 10/14/2010] [Indexed: 11/28/2022]
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176
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Bergmann I, Nettmann E, Mundt K, Klocke M. Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis. Can J Microbiol 2010; 56:440-4. [PMID: 20555406 DOI: 10.1139/w10-021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Energy production of renewable raw material is of increasing importance for sustainable energy production. As an indispensable prerequirement for further upgrading of technical equipment and operation modes of biogas plants, a deeper knowledge of the microbial community responsible for methane formation is crucial. To overcome these limitations a mesophilic biogas plant converting pig manure, maize silage, and grains of crop was sampled and subsequently analysed by construction of a methanogenic Archaea specific 16S rRNA gene clone library combined with PCR-RFLP analysis and group-specific quantitative real-time PCR (qPCR). Seventy percent of all analysed clones belonged to the order Methanomicrobiales, whereas 13% belonged to Methanosarcinales, 6% belonged to the Methanobacteriales group, and 11% of all detected clones were assigned to the CA11 and Arch1 cluster. Comparable percentages were obtained with qPCR: 84% of all detected 16S rRNA gene copy numbers were affiliated with the Methanomicrobiales, while only 14% belonged to the Methanosarcinales and 2% to the Methanobacteriales order. In conclusion, both approaches detected similar archaeal groups and revealed nearly the same abundance, pointing to a predominance of hydrogenotrophic methanogens in the biogas plant.
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Affiliation(s)
- I Bergmann
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany
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177
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Correlations between molecular and operational parameters in continuous lab-scale anaerobic reactors. Appl Microbiol Biotechnol 2010; 89:303-14. [DOI: 10.1007/s00253-010-2858-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 08/02/2010] [Accepted: 08/19/2010] [Indexed: 01/03/2023]
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178
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Feng XM, Karlsson A, Svensson BH, Bertilsson S. Impact of trace element addition on biogas production from food industrial waste - linking process to microbial communities. FEMS Microbiol Ecol 2010; 74:226-40. [DOI: 10.1111/j.1574-6941.2010.00932.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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179
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Krakat N, Westphal A, Satke K, Schmidt S, Scherer P. The microcosm of a biogas fermenter: Comparison of moderate hyperthermophilic (60°C) with thermophilic (55°C) conditions. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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180
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Robinson CJ, Bohannan BJM, Young VB. From structure to function: the ecology of host-associated microbial communities. Microbiol Mol Biol Rev 2010; 74:453-76. [PMID: 20805407 PMCID: PMC2937523 DOI: 10.1128/mmbr.00014-10] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.
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Affiliation(s)
- Courtney J. Robinson
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
| | - Brendan J. M. Bohannan
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
| | - Vincent B. Young
- Department of Internal Medicine, Division of Infectious Diseases, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon 97403
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181
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Shin SG, Han G, Lim J, Lee C, Hwang S. A comprehensive microbial insight into two-stage anaerobic digestion of food waste-recycling wastewater. WATER RESEARCH 2010; 44:4838-49. [PMID: 20678786 DOI: 10.1016/j.watres.2010.07.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Revised: 06/14/2010] [Accepted: 07/08/2010] [Indexed: 05/05/2023]
Abstract
Microbial community structures were assessed in a two-stage anaerobic digestion system treating food waste-recycling wastewater. The reactors were operated for 390 d at 10 different hydraulic retention times (HRTs) ranging from 25 to 4 d. Stable operation was achieved with the overall chemical oxygen demand (COD) removal efficiency of 73.0-85.9% at organic loading rate of up to 35.6 g COD/L·d. Performance of the acidogenic reactors, however, changed significantly during operation. This change coincided with transition of the bacterial community from one dominated by Aeriscardovia- and Lactobacillus amylovorus-related species to one dominated by Lactobacillus acetotolerans- and Lactobacillus kefiri-like organisms. In methanogenic reactors, the microbial community structures also changed at this stage along with the shift from Methanoculleus- to Methanosarcina-like organisms. This trend was confirmed by the non-metric multidimensional scaling joint plot of microbial shifts along with performance parameters. These results indicated that the overall process performance was relatively stable compared to the dynamic changes in the microbial structures and the acidogenic performance.
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Affiliation(s)
- Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
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182
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Wang X, Wen X, Criddle C, Yan H, Zhang Y, Ding K. Bacterial community dynamics in two full-scale wastewater treatment systems with functional stability. J Appl Microbiol 2010; 109:1218-26. [PMID: 20477893 DOI: 10.1111/j.1365-2672.2010.04742.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the bacterial community dynamics over 1 year in two full-scale wastewater treatment systems operated under constant conditions and exhibiting stable performance. METHODS AND RESULTS Functional stability was defined and quantified by the effluent concentration of biological oxygen demand, total nitrogen and ammonia. Community dynamics were investigated using specific PCR followed by terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. The T-RFLP results indicated that during the period of functional stability, the bacterial community structures in two full-scale wastewater treatment systems were not stable, and the average change rates every 15 days of the two systems were 22.6 ± 6.9 and 21.6 ± 7.3%, respectively. The corresponding species with dominant T-RFs were determined by clonal sequencing and T-RFLP. Based on Pareto-Lorenz distribution curves, it was observed that only a small number of micro-organisms were numerically dominant in the two systems. CONCLUSIONS The results of this study showed that, throughout the period of the study, the bacterial community structure changed significantly in two full-scale wastewater treatment systems despite the stable function. SIGNIFICANCE AND IMPACT OF THE STUDY The findings enrich the theory involving the relation between bacterial community dynamics and functional stability in full-scale wastewater treatment plants.
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Affiliation(s)
- X Wang
- Environmental Simulation and Pollution Control State Key Joint Laboratory, Department of Environmental Science and Engineering, Tsinghua University, Beijing, China
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183
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Kovacik WP, Scholten JCM, Culley D, Hickey R, Zhang W, Brockman FJ. Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed. Microbiology (Reading) 2010; 156:2418-2427. [DOI: 10.1099/mic.0.036715-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The upflow anaerobic sludge blanket (UASB) reactor is a microcosm for the methanogenic degradation of organic matter in anaerobic environments, and depends on the auto-formation of dense 3D biofilms of 1–3 mm in diameter, referred to as granular sludge (biogranules). Past research has shown that UASB and other methanogenic reactors are extremely stable functionally, but the underlying basis of the functional stability is not well understood. In this study, microbial dynamics in the communities residing in UASB biogranules were analysed to determine responses to short-term perturbations (change in reactor feed). The reactor was fed with simulated brewery wastewater (SBWW) for 1.5 months (phase 1), acetate/sulfate for 2 months (phase 2), acetate alone for 3 months (phase 3) and then a return to SBWW for 2 months (phase 4). Analysis of 16S rRNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB gene-based-clone libraries showed a relatively simple community composed mainly of the methanogenic archaea (Methanobacterium and Methanosaeta), members of the green non-sulfur (Chloroflexi) group of bacteria and Syntrophobacter, Spirochaeta, Acidobacteria and Cytophaga-related bacterial sequences. The mcrA clone libraries were dominated throughout by Methanobacterium- and Methanospirillum-related sequences. Although the reactor performance remained relatively stable throughout the experiment, community diversity levels generally decreased for all libraries in response to a change from SBWW to acetate alone feed. There was a large transitory increase noted in 16S diversity at the 2 month sampling on acetate alone, entirely related to an increase in bacterial diversity. Upon return to SBWW conditions in phase 4, all diversity measures returned to near phase 1 levels. Our results demonstrated that microbial communities, even highly structured ones such as in UASB biogranules, are very capable of responding to rapid and major changes in their environment.
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Affiliation(s)
- William P. Kovacik
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - David Culley
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Weiwen Zhang
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Fred J. Brockman
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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184
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Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production. Appl Microbiol Biotechnol 2010; 88:389-99. [DOI: 10.1007/s00253-010-2789-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/09/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
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185
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Bacterial community and "Candidatus Accumulibacter" population dynamics in laboratory-scale enhanced biological phosphorus removal reactors. Appl Environ Microbiol 2010; 76:5479-87. [PMID: 20601516 DOI: 10.1128/aem.00370-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Accumulibacter" and total bacterial community dynamics were studied in two lab-scale enhanced biological phosphorus removal (EBPR) reactors by using a community fingerprint technique, automated ribosomal intergenic spacer analysis (ARISA). We first evaluated the quantitative capability of ARISA compared to quantitative real-time PCR (qPCR). ARISA and qPCR provided comparable relative quantification of the two dominant "Ca. Accumulibacter" clades (IA and IIA) detected in our reactors. The quantification of total "Ca. Accumulibacter" 16S rRNA genes relative to that from the total bacterial community was highly correlated, with ARISA systematically underestimating "Ca. Accumulibacter" abundance, probably due to the different normalization techniques applied. During 6 months of normal (undisturbed) operation, the distribution of the two clades within the total "Ca. Accumulibacter" population was quite stable in one reactor while comparatively dynamic in the other reactor. However, the variance in the clade distribution did not appear to affect reactor performance. Instead, good EBPR activity was positively associated with the abundance of total "Ca. Accumulibacter." Therefore, we concluded that the different clades in the system provided functional redundancy. We disturbed the reactor operation by adding nitrate together with acetate feeding in the anaerobic phase to reach initial reactor concentrations of 10 mg/liter NO(3)-N for 35 days. The reactor performance deteriorated with a concomitant decrease in the total "Ca. Accumulibacter" population, suggesting that a population shift was the cause of performance upset after a long exposure to nitrate in the anaerobic phase.
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186
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Basile LA, Erijman L. Maintenance of phenol hydroxylase genotypes at high diversity in bioreactors exposed to step increases in phenol loading. FEMS Microbiol Ecol 2010; 73:336-48. [PMID: 20500527 DOI: 10.1111/j.1574-6941.2010.00898.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
To better understand how the composition of bacterial communities changes in response to different environmental conditions, we examined the influence of increasing phenol load on the distribution of the protein-coding functional gene of the largest subunit of phenol hydroxylase (LmPH) and of the 16S rRNA gene in lab-scale activated sludge reactors. LmPH diversity was assessed initially from a total of 124 clone sequences retrieved from two reactors exposed to a low (0.25 g L(-1)) and a high (2.5 g L(-1)) phenol concentration. The quantitative changes in the concentration of the eight detected genotypes accompanied changes in the phenol degradation rates, indicating a community structure-function relationship. Nonmetric dimensional analysis showed that LmPH genotypes and the denaturing gradient gel electrophoresis banding patterns clustered together by phenol concentration, rather than by reactor identity. Seven isolates, representing cultivated strains of each of the observed LmPH genotypes, exhibited a rather narrow range of physiological diversity, in terms of the growth rate and the kinetic parameters of the phenol-degrading activity. We suggest that lab-scale reactors support many ecological niches, which allow the maintenance of a high diversity of ecotypes through varying concentrations of phenol, but the ability of particular strains to become dominant members of the community under the different environmental conditions cannot be predicted easily solely from their phenol-degrading properties.
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Affiliation(s)
- Laura A Basile
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
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187
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Miller LD, Mosher JJ, Venkateswaran A, Yang ZK, Palumbo AV, Phelps TJ, Podar M, Schadt CW, Keller M. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiol 2010; 10:149. [PMID: 20497531 PMCID: PMC2906461 DOI: 10.1186/1471-2180-10-149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 05/24/2010] [Indexed: 01/03/2023] Open
Abstract
Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.
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Affiliation(s)
- Lance D Miller
- Biosciences and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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188
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Vallino JJ. Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production. Philos Trans R Soc Lond B Biol Sci 2010; 365:1417-27. [PMID: 20368260 PMCID: PMC2871896 DOI: 10.1098/rstb.2009.0272] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we use a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyse reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space-time, which we refer to as the steepest descent pathway. It is the spatio-temporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self-organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.
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Affiliation(s)
- Joseph J Vallino
- Marine Biological Laboratory, Ecosystems Center, Woods Hole, MA 02543, USA.
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189
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Ayarza JM, Guerrero LD, Erijman L. Nonrandom assembly of bacterial populations in activated sludge flocs. MICROBIAL ECOLOGY 2010; 59:436-444. [PMID: 19756849 DOI: 10.1007/s00248-009-9581-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 08/17/2009] [Indexed: 05/28/2023]
Abstract
The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were analyzed during a period of up to ten SRT, using denaturing gradient gel electrophoresis (DGGE) of reverse-transcription polymerase chain reaction-amplified 16S rRNA. High rates of change in DGGE profiles from consecutive sampling points suggested a high level of dynamics in all reactors. This conclusion was confirmed by the application of the Raup and Crick probability-based similarity index (S(RC)) for the comparison of rRNA-based fingerprinting patterns, which indicated that bacterial communities within reactors were not significantly similar after three SRT (0.05 < S(RC) < 0.95) and became significantly dissimilar after five SRT (S(RC) < 0.05). More importantly, significant similarity between replicate reactors was observed at all times analyzed (S(RC) > 0.95). The fact that the patterns between replicates were more reproducible than expected by chance under highly dynamic conditions allowed us to reject the null hypothesis that activated sludge floc communities assemble randomly from the available source pool of bacteria. We suggest that communities progressively recruit from the available pool of bacterial species, each with particular ecological requirements that determine their time of emergence into the community.
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Affiliation(s)
- Joaquín M Ayarza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Vuelta de Obligado 2490 (C1428ADN), Buenos Aires, Argentina
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190
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Nettmann E, Bergmann I, Pramschüfer S, Mundt K, Plogsties V, Herrmann C, Klocke M. Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 2010; 76:2540-8. [PMID: 20154117 PMCID: PMC2849221 DOI: 10.1128/aem.01423-09] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 02/02/2010] [Indexed: 11/20/2022] Open
Abstract
Knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic Archaea in the reactor samples. In addition, quantitative real-time PCR (Q-PCR) was used to support and complete the FISH analysis. Five of the six biogas reactors were dominated by hydrogenotrophic Methanomicrobiales. The average values were between 60 to 63% of archaeal cell counts (FISH) and 61 to 99% of archaeal 16S rRNA gene copies (Q-PCR). Within this order, Methanoculleus was found to be the predominant genus as determined by amplified rRNA gene restriction analysis. The aceticlastic family Methanosaetaceae was determined to be the dominant methanogenic group in only one biogas reactor, with average values for Q-PCR and FISH between 64% and 72%. Additionally, in three biogas reactors hitherto uncharacterized but potentially methanogenic species were detected. They showed closest accordance with nucleotide sequences of the hitherto unclassified CA-11 (85%) and ARC-I (98%) clusters. These results point to hydrogenotrophic methanogenesis as a predominant pathway for methane synthesis in five of the six analyzed biogas plants. In addition, a correlation between the absence of Methanosaetaceae in the biogas reactors and high concentrations of total ammonia (sum of NH(3) and NH(4)(+)) was observed.
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MESH Headings
- Ammonia/metabolism
- Archaea/classification
- Archaea/genetics
- Archaea/metabolism
- Biofuels/microbiology
- Bioreactors/microbiology
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Hydrogen/metabolism
- In Situ Hybridization, Fluorescence
- Methane/metabolism
- Molecular Sequence Data
- RNA, Archaeal/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- E. Nettmann
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - I. Bergmann
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - S. Pramschüfer
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - K. Mundt
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - V. Plogsties
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - C. Herrmann
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
| | - M. Klocke
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Technikbewertung und Stoffkreisläufe, Max-Eyth-Allee 100, D-14469 Potsdam, Germany, Technische Universität Berlin, Fakultät 3, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, D-10587 Berlin, Germany, Beuth Hochschule für Technik Berlin, Fachbereich Life Sciences and Technology, Lütticher Straße 38, D-13353 Berlin, Germany, Humboldt Universität zu Berlin, Landwirtschaftlich-Gärtnerische Fakultät, Invalidenstraße 42, D-10099 Berlin, Germany
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191
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Obernosterer I, Lami R, Larcher M, Batailler N, Catala P, Lebaron P. Linkage between bacterial carbon processing and the structure of the active bacterial community at a coastal site in the NW Mediterranean Sea. MICROBIAL ECOLOGY 2010; 59:428-435. [PMID: 19789909 DOI: 10.1007/s00248-009-9588-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 09/01/2009] [Indexed: 05/28/2023]
Abstract
The temporal dynamics in bulk bacterial parameters and in the richness of the total and active bacterial community, determined from CE-SSCP fingerprints of 16S rRNA genes and 16S rRNA transcripts, respectively, were followed weekly to bimonthly at an oligotrophic coastal site in the NW Mediterranean Sea. Bacterial abundance, bacterial heterotrophic production, and bacterial and community respiration determined over two seasonal cycles displayed large short-term variability and no pronounced temporal pattern was detectable for these parameters. Concentrations in inorganic nutrients, salinity, or concentrations of chlorophyll a could not significantly explain the temporal variability of the bacterial parameters determined. By contrast, bacterial respiration and the bacterial carbon demand were both negatively correlated with the richness of the active bacterial community, while the bacterial parameters determined herein were not related to the richness of the total bacterial community present. Our results indicate that a reduced number of ribotypes is active when rates of bacteria-mediated carbon processes are high. Our approach, based on fingerprints of 16S rRNA transcripts, could represent an interesting tool to investigate the relationship between the structure and function of marine bacteria, in particular, on short temporal and spatial scales.
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Affiliation(s)
- Ingrid Obernosterer
- UPMC Univ Paris 06, UMR 7621, LOBB, Observatoire Océanologique, F-66651, Banyuls/mer, France.
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192
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Trzcinski AP, Ray MJ, Stuckey DC. Performance of a three-stage membrane bioprocess treating the organic fraction of municipal solid waste and evolution of its archaeal and bacterial ecology. BIORESOURCE TECHNOLOGY 2010; 101:1652-1661. [PMID: 19857960 DOI: 10.1016/j.biortech.2009.09.075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 09/20/2009] [Accepted: 09/23/2009] [Indexed: 05/28/2023]
Abstract
A novel three-stage bioprocess achieved 75% volatile solids (VS) removal at an organic loading rate (OLR) of 4g VSL(-1)day, a solids retention time (SRT) of 66days, a hydraulic retention time (HRT) of 20days, at a temperature of 35 degrees C. The bioprocess consisted of an anaerobic hydrolytic reactor (HR) where the solids and liquid fractions of the Organic Fraction of the Municipal Solid Waste (OFMSW) were separated with a mesh. The leachate was pumped to a Submerged Anaerobic Membrane Bioreactor (SAMBR) and the treated permeate was polished in an Aerobic Membrane Bioreactor (AMBR). Denaturing Gradient Gel Electrophoresis (DGGE) and DNA sequencing analyses indicated that the increase in methane content in the HR caused by the excess sludge recycle from the SAMBR was associated with an increase in the number of hydrogenotrophic species, mainly Methanobrevibacter sp., Methanobacterium formicicum and Methanosarcina sp. At 20 degrees C VS removal dropped to 50% in the HR and some DGGE bands disappeared when compared to 35 degrees C samples, while some bands such as the one corresponding to Ruminococcus flavefaciens were reduced in intensity. The species associated with the COD-polishing properties of the AMBR correspond to the genera Pseudomonas, Hyphomonas and Hyphomicrobiaceae. These results highlight the positive effect of recycling the excess sludge from the SAMBR to re-inoculate the HR with hydrogenotrophic species.
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Affiliation(s)
- Antoine P Trzcinski
- Department of Chemical Engineering, Imperial College of Science and Technology and Medicine, Prince Consort Road, London SW7 2AZ, UK.
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193
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AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME JOURNAL 2010; 4:599-610. [PMID: 20164865 DOI: 10.1038/ismej.2009.158] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.
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194
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Past, Present, and Future: Microbial Mats as Models for Astrobiological Research. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2010. [DOI: 10.1007/978-90-481-3799-2_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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195
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Wojnowska-Baryła I, Cydzik-Kwiatkowska A, Zielińska M. The application of molecular techniques to the study of wastewater treatment systems. Methods Mol Biol 2010; 599:157-183. [PMID: 19882286 DOI: 10.1007/978-1-60761-439-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Wastewater treatment systems tend to be engineered to select for a few functional microbial groups that may be organized in various spatial structures such as activated sludge flocs, biofilm or granules and represented by single coherent phylogenic groups such as ammonia-oxidizing bacteria (AOB) and polyphosphate-accumulating organisms (PAO). In order to monitor and control engineered microbial structure in wastewater treatment systems, it is necessary to understand the relationships between the microbial community structure and the process performance. This review focuses on bacterial communities in wastewater treatment processes, the quantity of microorganisms and structure of microbial consortia in wastewater treatment bioreactors. The review shows that the application of molecular techniques in studies of engineered environmental systems has increased our insight into the vast diversity and interaction of microorganisms present in wastewater treatment systems.
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Affiliation(s)
- Irena Wojnowska-Baryła
- Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Sloneczna, Poland
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196
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Wu XL, Chin KJ, Conrad R. Effect of temperature stress on structure and function of the methanogenic archaeal community in a rice field soil. FEMS Microbiol Ecol 2009; 39:211-8. [PMID: 19709200 DOI: 10.1111/j.1574-6941.2002.tb00923.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The effect of a brief (24 h) temperature shift to 4 degrees C (low-temperature stress) or 50 degrees C (high-temperature stress) was studied in methanogenic slurries of Italian rice field soil incubated at either constant 30 degrees C or 15 degrees C. Low-temperature (low-T) stress showed no effect in either the 30 degrees C or the 15 degrees C incubations. High-temperature (high-T) stress, on the other hand, generally resulted in an increase in the partial pressure of H(2), and the concentrations of acetate and propionate, which accumulated to about 100-200 Pa, 4-6 mM and 0.7-0.9 mM, respectively. The increase in H(2) was transient for 8-15 days. The increases in acetate and propionate were transient for about 20 days only in the 30 degrees C incubations, but persisted in the 15 degrees C incubations until the end of the experiment. The high-T stress did not result in inhibition of CH(4) production in the 30 degrees C incubations, but transiently inhibited the 15 degrees C incubations for about 25-30 days. The archaeal community in the soils was analyzed by terminal restriction fragment length polymorphism of the gene of the SSU rRNA. In the 15 degrees C incubations, the relative gene frequency of members of the Methanosarcinaceae decreased over an incubation period of 54 days, while those of Methanosaetaceae and of methanogenic rice cluster I increased. Temperature stress, high-T stress in particular, tended to reverse this trend. In the 30 degrees C incubations, on the other hand, the relative gene frequency of archaeal members showed the opposite temporal trend or remained constant unlike the 15 degrees C incubations. Again, high-T stress tended to reverse these trends, but the observed effects were much smaller in the 30 degrees C incubations than in the 15 degrees C incubations. In conclusion, a brief high-T stress affected structure and function of the methanogenic archaeal community of rice field soil.
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Affiliation(s)
- Xiao-Lei Wu
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str., 35043 Marburg, Germany
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197
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Franke-Whittle IH, Goberna M, Pfister V, Insam H. Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities. J Microbiol Methods 2009; 79:279-88. [DOI: 10.1016/j.mimet.2009.09.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 09/18/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
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198
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Michelland R, Monteils V, Zened A, Combes S, Cauquil L, Gidenne T, Hamelin J, Fortun-Lamothe L. Spatial and temporal variations of the bacterial community in the bovine digestive tract. J Appl Microbiol 2009; 107:1642-50. [DOI: 10.1111/j.1365-2672.2009.04346.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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199
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Nettmann E, Bergmann I, Mundt K, Linke B, Klocke M. Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J Appl Microbiol 2009; 105:1835-50. [PMID: 19120632 DOI: 10.1111/j.1365-2672.2008.03949.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The Archaea diversity was evaluated in an agricultural biogas plant supplied with cattle liquid manure and maize silage under mesophilic conditions. METHODS AND RESULTS Two different genes (16S rRNA; methyl-coenzyme-M-reductase, MCR) targeted by three different PCR primer sets were selected and used for the construction of three clone libraries comprising between 104 and 118 clones. The clone libraries were analysed by restriction fragment polymorphism (RFLP). Between 11 and 31 operational taxonomic units (OTUs) were detected and assigned to orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. Over 70% of all Archaea OTUs belong to the order Methanomicrobiales which mostly include hydrogenotrophic methanogens. Acetotrophic methanogens were detected in minor rates. Similar relative values were obtained by a quantitative real-time PCR analysis. CONCLUSIONS The results implied that in this biogas plant the most of the methane formation resulted from the conversion of H(2) and CO(2). SIGNIFICANCE AND IMPACT OF THE STUDY This study reports, for the first time, a molecular analysis of the archaeal community in this type of agricultural biogas plants. Therein the hydrogenotrophic methanogenesis seems to be the major pathway of methane formation. These results are in contrast with the common thesis that in biogas fermentations the primary substrate for methanogenesis is acetate.
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Affiliation(s)
- E Nettmann
- Leibniz-Institut für Agrartechnik Potsdam-Bornim eV, Abteilung Bioverfahrenstechnik, Potsdam-Bornim, Germany
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200
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Novel electrochemically active bacterium phylogenetically related to Arcobacter butzleri, isolated from a microbial fuel cell. Appl Environ Microbiol 2009; 75:7326-34. [PMID: 19801475 DOI: 10.1128/aem.01345-09] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Exoelectrogenic bacteria are organisms that can transfer electrons to extracellular insoluble electron acceptors and have the potential to be used in devices such as microbial fuel cells (MFCs). Currently, exoelectrogens have been identified in the Alpha-, Beta-, Gamma- and Deltaproteobacteria, as well as in the Firmicutes and Acidobacteria. Here, we describe use of culture-independent methods to identify two members of the genus Arcobacter in the Epsilonproteobacteria that are selectively enriched in an acetate-fed MFC. One of these organisms, Arcobacter butzleri strain ED-1, associates with the electrode and rapidly generates a strong electronegative potential as a pure culture when it is supplied with acetate. A mixed-community MFC in which approximately 90% of the population is comprised of the two Arcobacter species generates a maximal power density of 296 mW/liter. This demonstration of exoelectrogenesis by strain ED-1 is the first time that this property has been shown for members of this genus.
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