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Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing. mBio 2023; 14:e0358422. [PMID: 36877031 PMCID: PMC10128055 DOI: 10.1128/mbio.03584-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.
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Schwarz E, Khurana S, Chakrawal A, Chavez Rodriguez L, Wirsching J, Streck T, Manzoni S, Thullner M, Pagel H. Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14427-14438. [PMID: 36166755 PMCID: PMC9583605 DOI: 10.1021/acs.est.2c03397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/12/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Microbial pesticide degraders are heterogeneously distributed in soil. Their spatial aggregation at the millimeter scale reduces the frequency of degrader-pesticide encounter and can introduce transport limitations to pesticide degradation. We simulated reactive pesticide transport in soil to investigate the fate of the widely used herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in response to differently aggregated distributions of degrading microbes. Four scenarios were defined covering millimeter scale heterogeneity from homogeneous (pseudo-1D) to extremely heterogeneous degrader distributions and two precipitation scenarios with either continuous light rain or heavy rain events. Leaching from subsoils did not occur in any scenario. Within the topsoil, increasing spatial heterogeneity of microbial degraders reduced macroscopic degradation rates, increased MCPA leaching, and prolonged the persistence of residual MCPA. In heterogeneous scenarios, pesticide degradation was limited by the spatial separation of degrader and pesticide, which was quantified by the spatial covariance between MCPA and degraders. Heavy rain events temporarily lifted these transport constraints in heterogeneous scenarios and increased degradation rates. Our results indicate that the mild millimeter scale spatial heterogeneity of degraders typical for arable topsoil will have negligible consequences for the fate of MCPA, but strong clustering of degraders can delay pesticide degradation.
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Affiliation(s)
- Erik Schwarz
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Swamini Khurana
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
| | - Arjun Chakrawal
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
| | - Luciana Chavez Rodriguez
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
- Department
of Ecology and Evolutionary Biology, University
of California Irvine, Irvine, California 92697, United States
| | - Johannes Wirsching
- Institute
of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Thilo Streck
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Stefano Manzoni
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
| | - Martin Thullner
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
- Federal
Institute for Geosciences and Natural Resources (BGR), 30655 Hannover, Germany
| | - Holger Pagel
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
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3
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An S, Kim K, Woo H, Yun ST, Chung J, Lee S. Coupled effect of porous network and water content on the natural attenuation of diesel in unsaturated soils. CHEMOSPHERE 2022; 302:134804. [PMID: 35533929 DOI: 10.1016/j.chemosphere.2022.134804] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
The natural attenuation potential of a vadose zone against diesel is critical for optimizing remedial actions and determining groundwater vulnerability to contamination. Here, diesel attenuation in unsaturated soils was systematically examined to develop a qualitative relationship between physical soil properties and the natural attenuation capacity of a vadose zone against diesel. The uniformity coefficient (Cu) and water saturation (Sw, %) were considered as the proxies reflecting the degree of effects by porous network and water content in different soils, respectively. These, in turn, are related to the primary diesel attenuation mechanisms of volatilization and biodegradation. The volatilization of diesel was inversely proportional to Cu and Sw, which could be attributed to effective pore channels facilitating gas transport. Conversely, biodegradation was highly proportional to Cu under unsaturated conditions (Sw = 35-71%), owing to nutrients typically associated with fine soil particles. The microbial community in unsaturated soils was affected by Sw rather than Cu. The overall diesel attenuation including volatilization and biodegradation was optimized at Sw = 35% for all tested soils.
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Affiliation(s)
- Seongnam An
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Department of Earth and Environmental Sciences, Korea University, Seoul, 136-701, South Korea
| | - Kibeum Kim
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
| | - Heesoo Woo
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
| | - Seong-Taek Yun
- Department of Earth and Environmental Sciences, Korea University, Seoul, 136-701, South Korea
| | - Jaeshik Chung
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Division of Energy and Environmental Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, South Korea.
| | - Seunghak Lee
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea; Division of Energy and Environmental Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, South Korea; Graduate School of Energy and Environment (KU-KIST GREEN SCHOOL), Korea University, Seoul, 02841, South Korea.
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4
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Morita H, Akao S. The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks. PLoS One 2021; 16:e0260121. [PMID: 34793564 PMCID: PMC8601499 DOI: 10.1371/journal.pone.0260121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022] Open
Abstract
To determine the optimal soil sample size for microbial community structure analysis, DNA extraction, microbial composition analysis, and diversity assessments were performed using soil sample sizes of 0.2, 1, and 5 g. This study focused on the relationship between soil amount and DNA extraction container volume and the alteration in microbial composition at different taxonomic ranks (order, class, and phylum). Horizontal (0.2 and 1 g) and vertical (5 g) shaking were applied during DNA extraction for practical use in a small laboratory. In the case of the 5 g soil sample, DNA extraction efficiency and the value of α-diversity index fluctuated severely, possibly because of vertical shaking. Regarding the 0.2 and 1 g soil samples, the number of taxa, Shannon–Wiener index, and Bray–Curtis dissimilarity were stable and had approximately the same values at each taxonomic rank. However, non-metric multidimensional scaling showed that the microbial compositions of these two sample sizes were different. The higher relative abundance of taxa in the case of the 0.2 g soil sample might indicate that cell wall compositions differentiated the microbial community structures in these two sample sizes due to high shear stress tolerance. The soil sample size and tube volume affected the estimated microbial community structure. A soil sample size of 0.2 g would be preferable to the other sample sizes because of the possible higher shearing force for DNA extraction and lower experimental costs due to smaller amounts of consumables. When the taxonomic rank was changed from order to phylum, some minor taxa identified at the order rank were integrated into major taxa at the phylum rank. The integration affected the value of the β-diversity index; therefore, the microbial community structure analysis, reproducibility of structures, diversity assessment, and detection of minor taxa would be influenced by the taxonomic rank applied.
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Affiliation(s)
- Hiroki Morita
- Graduate School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Satoshi Akao
- Graduate School of Science and Engineering, Doshisha University, Kyotanabe, Kyoto, Japan
- * E-mail:
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5
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Wirsching J, Pagel H, Ditterich F, Uksa M, Werneburg M, Zwiener C, Berner D, Kandeler E, Poll C. Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations. Front Microbiol 2020; 11:2107. [PMID: 32983068 PMCID: PMC7481373 DOI: 10.3389/fmicb.2020.02107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/10/2020] [Indexed: 11/15/2022] Open
Abstract
The objective of our study was to test whether limited microbial degradation at low pesticide concentrations could explain the discrepancy between overall degradability demonstrated in laboratory tests and their actual persistence in the environment. Studies on pesticide degradation are often performed using unrealistically high application rates seldom found in natural environments. Nevertheless, biodegradation rates determined for higher pesticide doses cannot necessarily be extrapolated to lower concentrations. In this context, we wanted to (i) compare the kinetics of pesticide degradation at different concentrations in arable land and (ii) clarify whether there is a concentration threshold below which the expression of the functional genes involved in the degradation pathway is inhibited without further pesticide degradation taking place. We set up an incubation experiment for four weeks using 14C-ring labeled 2-methyl-4-chlorophenoxyacetic acid (MCPA) as a model compound in concentrations from 30 to 20,000 μg kg–1 soil. To quantify the abundance of putative microorganisms involved in MCPA degradation and their degradation activity, tfdA gene copy numbers (DNA) and transcripts (mRNA) were determined by quantitative real-time PCR. Mineralization dynamics of MCPA derived-C were analyzed by monitoring 14CO2 production and 14C assimilation by soil microorganisms. We identified two different concentration thresholds for growth and activity with respect to MCPA degradation using tfdA gene and mRNA transcript abundance as growth and activity indices, respectively. The tfdA gene expression started to increase between 1,000 and 5,000 μg MCPA kg–1 dry soil, but an actual increase in tfdA sequences could only be determined at a concentration of 20,000 μg. Accordingly, we observed a clear shift from catabolic to anabolic utilization of MCPA-derived C in the concentration range of 1,000 to 5,000 μg kg–1. Concentrations ≥1,000 μg kg–1 were mainly associated with delayed mineralization, while concentrations ≤1,000 μg kg–1 showed rapid absolute dissipation. The persistence of pesticides at low concentrations cannot, therefore, be explained by the absence of functional gene expression. Nevertheless, significant differences in the degradation kinetics of MCPA between low and high pesticide concentrations illustrate the need for studies investigating pesticide degradation at environmentally relevant concentrations.
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Affiliation(s)
- Johannes Wirsching
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Holger Pagel
- Department of Soil Physics, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Franziska Ditterich
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Marie Uksa
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Martina Werneburg
- Department of Environmental Analytical Chemistry, Institute of Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Christian Zwiener
- Department of Environmental Analytical Chemistry, Institute of Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Doreen Berner
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Christian Poll
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
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Worrich A, Wick LY, Banitz T. Ecology of Contaminant Biotransformation in the Mycosphere: Role of Transport Processes. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:93-133. [PMID: 30143253 DOI: 10.1016/bs.aambs.2018.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fungi and bacteria often share common microhabitats. Their co-occurrence and coevolution give rise to manifold ecological interactions in the mycosphere, here defined as the microhabitats surrounding and affected by hyphae and mycelia. The extensive structure of mycelia provides ideal "logistic networks" for transport of bacteria and matter in structurally and chemically heterogeneous soil ecosystems. We describe the characteristics of the mycosphere as a unique and highly dynamic bacterial habitat and a hot spot for contaminant biotransformation. In particular, we emphasize the role of the mycosphere for (i) bacterial dispersal and colonization of subsurface interfaces and new habitats, (ii) matter transport processes and contaminant bioaccessibility, and (iii) the functional stability of microbial ecosystems when exposed to environmental fluctuations such as stress or disturbances. Adopting concepts from ecological theory, the chapter disentangles bacterial-fungal impacts on contaminant biotransformation in a systemic approach that interlinks empirical data from microbial ecosystems with simulation data from computational models. This approach provides generic information on key factors, processes, and ecological principles that drive microbial contaminant biotransformation in soil. We highlight that the transport processes create favorable habitat conditions for efficient bacterial contaminant degradation in the mycosphere. In-depth observation, understanding, and prediction of the role of mycosphere transport processes will support the use of bacterial-fungal interactions in nature-based solutions for contaminant biotransformation in natural and man-made ecosystems, respectively.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany.
| | - Thomas Banitz
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
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7
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Effects of habitat constraints on soil microbial community function. Sci Rep 2017; 7:4280. [PMID: 28655916 PMCID: PMC5487364 DOI: 10.1038/s41598-017-04485-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
An underlying assumption of most soil carbon (C) dynamics models is that soil microbial communities are functionally similar; in other words, that microbial activity under given conditions is not dependent on the composition or diversity of the communities. Although a number of studies have indicated that microbial communities are not intrinsically functionally similar, most soil C dynamics models can adequately describe C dynamics without explicitly describing microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that the environmental context (soil and pore-network properties) of microbial communities can constrain the activity of functionally different communities to such an extent that their activities are indistinguishable. The data also suggest that when microbial activity is less constrained, the intrinsic functional differences among communities can be expressed. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments where their activity is less constrained, such as the rhizosphere or the litter layer, but not in oligotrophic environments such as the mineral layers of soil.
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8
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Worrich A, Stryhanyuk H, Musat N, König S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Richnow HH, Miltner A, Kästner M, Wick LY. Mycelium-mediated transfer of water and nutrients stimulates bacterial activity in dry and oligotrophic environments. Nat Commun 2017; 8:15472. [PMID: 28589950 PMCID: PMC5467244 DOI: 10.1038/ncomms15472] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/29/2017] [Indexed: 12/22/2022] Open
Abstract
Fungal–bacterial interactions are highly diverse and contribute to many ecosystem processes. Their emergence under common environmental stress scenarios however, remains elusive. Here we use a synthetic microbial ecosystem based on the germination of Bacillus subtilis spores to examine whether fungal and fungal-like (oomycete) mycelia reduce bacterial water and nutrient stress in an otherwise dry and nutrient-poor microhabitat. We find that the presence of mycelia enables the germination and subsequent growth of bacterial spores near the hyphae. Using a combination of time of flight- and nanoscale secondary ion mass spectrometry (ToF- and nanoSIMS) coupled with stable isotope labelling, we link spore germination to hyphal transfer of water, carbon and nitrogen. Our study provides direct experimental evidence for the stimulation of bacterial activity by mycelial supply of scarce resources in dry and nutrient-free environments. We propose that mycelia may stimulate bacterial activity and thus contribute to sustaining ecosystem functioning in stressed habitats. The maintenance of bacterial and fungal activity is essential for ecosystem functioning, particularly in dry soils where the two phyla co-exist. Here, Worrich and colleagues show experimentally that mycelia traffic water and nutrients and thereby stimulate bacterial activity in stressful conditions.
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Affiliation(s)
- Anja Worrich
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Niculina Musat
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sara König
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Thomas Banitz
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Karin Frank
- Department of Ecological Modelling, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany.,University of Osnabrück, Institute for Environmental Systems Research, Barbarastaße 12, 49076 Osnabrück, Germany
| | - Martin Thullner
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Anja Miltner
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
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9
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Babey T, Vieublé-Gonod L, Rapaport A, Pinheiro M, Garnier P, de Dreuzy JR. Spatiotemporal simulations of 2,4-D pesticide degradation by microorganisms in 3D soil-core experiments. Ecol Modell 2017. [DOI: 10.1016/j.ecolmodel.2016.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Worrich A, König S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Miltner A, Wick LY, Kästner M. Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress. Front Microbiol 2016; 7:1214. [PMID: 27536297 PMCID: PMC4971104 DOI: 10.3389/fmicb.2016.01214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/21/2016] [Indexed: 11/13/2022] Open
Abstract
Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. Here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of osmotic potentials (ΔΨo) using model ecosystems exhibiting a heterogeneous distribution of the soil-borne bacterium Pseudomonas putida KT2440. Three systematically manipulated scenarios allowed us to cover the effects of (i) substrate diffusion, (ii) substrate diffusion and autonomous bacterial dispersal, and (iii) substrate diffusion and autonomous as well as mediated bacterial dispersal along glass fiber networks mimicking fungal hyphae. To quantify the relative importance of the different spatial processes, we compared these heterogeneous scenarios to a reference value obtained for each ΔΨo by means of a quasi-optimal scenario in which degraders were ab initio homogeneously distributed. Substrate diffusion as the sole spatial process was insufficient to counteract the disadvantage due to spatial degrader heterogeneity at ΔΨo ranging from 0 to -1 MPa. In this scenario, only 13.8-21.3% of the quasi-optimal biodegradation performance could be achieved. In the same range of ΔΨo values, substrate diffusion in combination with bacterial dispersal allowed between 68.6 and 36.2% of the performance showing a clear downwards trend with decreasing ΔΨo. At -1.5 MPa, however, this scenario performed worse than the diffusion scenario, possibly as a result of energetic disadvantages associated with flagellum synthesis and emerging requirements to exceed a critical population density to resist osmotic stress. Network-mediated bacterial dispersal kept biodegradation almost consistently high with an average of 70.7 ± 7.8%, regardless of the strength of the osmotic stress. We propose that especially fungal network-mediated bacterial dispersal is a key process to achieve high functionality of heterogeneous microbial ecosystems also at reduced osmotic potentials. Thus, mechanical stress by, for example, soil homogenization should be kept low in order to preserve fungal network integrity.
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Affiliation(s)
- Anja Worrich
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Environmental BiotechnologyLeipzig, Germany
| | - Sara König
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany
| | - Thomas Banitz
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological Modelling Leipzig, Germany
| | - Florian Centler
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Karin Frank
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute for Environmental Systems Research, University of OsnabrückOsnabrück, Germany
| | - Martin Thullner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Hauke Harms
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Anja Miltner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
| | - Lukas Y Wick
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Matthias Kästner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
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11
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Mycelium-Like Networks Increase Bacterial Dispersal, Growth, and Biodegradation in a Model Ecosystem at Various Water Potentials. Appl Environ Microbiol 2016; 82:2902-2908. [PMID: 26944849 DOI: 10.1128/aem.03901-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/02/2016] [Indexed: 11/20/2022] Open
Abstract
Fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. However, poor knowledge exists on the effects of dispersal networks at various osmotic (Ψo) and matric (Ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. Here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subsequent effects on growth and benzoate biodegradation at ΔΨo and ΔΨm values between 0 and -1.5 MPa. In a multiple-microcosm approach, we used a green fluorescent protein (GFP)-tagged derivative of the soil bacterium Pseudomonas putida KT2440 as a model organism and sodium benzoate as a representative of polar aromatic contaminants. We found that decreasing ΔΨo and ΔΨm values slowed bacterial dispersal in the system, leading to decelerated growth and benzoate degradation. In contrast, dispersal networks facilitated bacterial movement at ΔΨo and ΔΨm values between 0 and -0.5 MPa and thus improved the absolute biodegradation performance by up to 52 and 119% for ΔΨo and ΔΨm, respectively. This strong functional interrelationship was further emphasized by a high positive correlation between population dispersal, population growth, and degradation. We propose that dispersal networks may sustain the functionality of microbial ecosystems at low osmotic and matric potentials.
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12
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Stolpovsky K, Fetzer I, Van Cappellen P, Thullner M. Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations. FEMS Microbiol Ecol 2016; 92:fiw071. [DOI: 10.1093/femsec/fiw071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 12/14/2022] Open
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13
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Wolf AB, Rudnick MB, de Boer W, Kowalchuk GA. Early colonizers of unoccupied habitats represent a minority of the soil bacterial community. FEMS Microbiol Ecol 2015; 91:fiv024. [PMID: 25778508 DOI: 10.1093/femsec/fiv024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 11/14/2022] Open
Abstract
In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0-1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 h, with the genera Undibacterium, Pseudomonas and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.
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Affiliation(s)
- Alexandra B Wolf
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, U.S.A
| | - Max-Bernhard Rudnick
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Plant Health, Institute for Vegetable and Ornamental Crops, Großbeeren/Erfurt e.V., Theodor Echtermeyer Weg 1, D-14979 Großbeeren, Germany
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Soil Quality, Wageningen University, 6700AA Wageningen, the Netherlands
| | - George A Kowalchuk
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Ecological Science, Free University of Amsterdam, 1081 HV Amsterdam, the Netherlands Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
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14
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Dechesne A, Badawi N, Aamand J, Smets BF. Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications. Front Microbiol 2014; 5:667. [PMID: 25538691 PMCID: PMC4257087 DOI: 10.3389/fmicb.2014.00667] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/17/2014] [Indexed: 11/16/2022] Open
Abstract
Pesticide biodegradation is a soil microbial function of critical importance for modern agriculture and its environmental impact. While it was once assumed that this activity was homogeneously distributed at the field scale, mounting evidence indicates that this is rarely the case. Here, we critically examine the literature on spatial variability of pesticide biodegradation in agricultural soil. We discuss the motivations, methods, and main findings of the primary literature. We found significant diversity in the approaches used to describe and quantify spatial heterogeneity, which complicates inter-studies comparisons. However, it is clear that the presence and activity of pesticide degraders is often highly spatially variable with coefficients of variation often exceeding 50% and frequently displays non-random spatial patterns. A few controlling factors have tentatively been identified across pesticide classes: they include some soil characteristics (pH) and some agricultural management practices (pesticide application, tillage), while other potential controlling factors have more conflicting effects depending on the site or the pesticide. Evidence demonstrating the importance of spatial heterogeneity on the fate of pesticides in soil has been difficult to obtain but modeling and experimental systems that do not include soil's full complexity reveal that this heterogeneity must be considered to improve prediction of pesticide biodegradation rates or of leaching risks. Overall, studying the spatial heterogeneity of pesticide biodegradation is a relatively new field at the interface of agronomy, microbial ecology, and geosciences and a wealth of novel data is being collected from these different disciplinary perspectives. We make suggestions on possible avenues to take full advantage of these investigations for a better understanding and prediction of the fate of pesticides in soil.
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Affiliation(s)
- Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark Lyngby, Denmark
| | - Nora Badawi
- Department of Geochemistry, Geological Survey of Denmark and Greenland Copenhagen, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark and Greenland Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark Lyngby, Denmark
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15
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Coronado E, Roggo C, van der Meer JR. Identification of genes potentially involved in solute stress response in Sphingomonas wittichii RW1 by transposon mutant recovery. Front Microbiol 2014; 5:585. [PMID: 25408691 PMCID: PMC4219479 DOI: 10.3389/fmicb.2014.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/17/2014] [Indexed: 11/13/2022] Open
Abstract
The term water stress refers to the effects of low water availability on microbial growth and physiology. Water availability has been proposed as a major constraint for the use of microorganisms in contaminated sites with the purpose of bioremediation. Sphingomonas wittichii RW1 is a bacterium capable of degrading the xenobiotic compounds dibenzofuran and dibenzo-p-dioxin, and has potential to be used for targeted bioremediation. The aim of the current work was to identify genes implicated in water stress in RW1 by means of transposon mutagenesis and mutant growth experiments. Conditions of low water potential were mimicked by adding NaCl to the growth media. Three different mutant selection or separation method were tested which, however recovered different mutants. Recovered transposon mutants with poorer growth under salt-induced water stress carried insertions in genes involved in proline and glutamate biosynthesis, and further in a gene putatively involved in aromatic compound catabolism. Transposon mutants growing poorer on medium with lowered water potential also included ones that had insertions in genes involved in more general functions such as transcriptional regulation, elongation factor, cell division protein, RNA polymerase β or an aconitase.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Clémence Roggo
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
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16
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Bell CW, Tissue DT, Loik ME, Wallenstein MD, Acosta-Martinez V, Erickson RA, Zak JC. Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland. GLOBAL CHANGE BIOLOGY 2014; 20:1657-73. [PMID: 24115607 DOI: 10.1111/gcb.12418] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 09/07/2013] [Indexed: 05/23/2023]
Abstract
Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7-year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2-year delay in microbial responses to supplemental precipitation treatments. In years 3-5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5-7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long-term effects on nutrient cycling and plant P uptake in this desert grassland.
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Affiliation(s)
- Colin W Bell
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80524 - 1499, USA; Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409 - 3131, USA
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17
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Vos M, Wolf AB, Jennings SJ, Kowalchuk GA. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev 2013; 37:936-54. [DOI: 10.1111/1574-6976.12023] [Citation(s) in RCA: 338] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022] Open
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18
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Monard C, Mchergui C, Nunan N, Martin-Laurent F, Vieublé-Gonod L. Impact of soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities. FEMS Microbiol Ecol 2012; 81:673-83. [PMID: 22531018 DOI: 10.1111/j.1574-6941.2012.01398.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 04/19/2012] [Accepted: 04/19/2012] [Indexed: 11/29/2022] Open
Abstract
The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of (13) C-glucose and (13) C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (-0.001, -0.01 and -0.316 MPa) in 6 × 6 × 6 mm(3) cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.
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Affiliation(s)
- Cécile Monard
- INRA, UMR 1091 Environnement et Grandes Cultures, Bâtiment EGER, Thiverval Grignon, France
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19
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Pseudomonad swarming motility is restricted to a narrow range of high matric water potentials. Appl Environ Microbiol 2012; 78:2936-40. [PMID: 22327576 DOI: 10.1128/aem.06833-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using a novel experimental system that allows control of the matric potential of an agar slab, we explored the hydration conditions under which swarming motility is possible. If there is recognition that this physical parameter is a key determinant of swarming, it is usually neither controlled nor measured rigorously but only manipulated through proxies, namely, the agar concentration and the drying time of "soft" agar plates (swarming plates). We contend that this not only obscures the biophysical mechanisms underlying swarming but also impedes a full assessment of its clinical and environmental significances. Our results indicate that swarming motility is restricted to a narrow range of high matric water potentials in the three pseudomonads tested (Pseudomonas sp. DSS73, Pseudomonas syringae B728a, and Pseudomonas aeruginosa PA14). The threshold below which no swarming was observed was about -0.45 kPa for the first and about -0.1 kPa for the latter two. Above the threshold, the expansion rate of DSS73 swarms increased exponentially with the matric potential. Mutants deficient in surfactant production were totally or partially unable to expand rapidly on the surface of the agar slab. Our results thus suggest that swarming motility in pseudomonads is restricted to (micro)sites where ambient humidity is very high (relative humidity of >99.99%). The spatiotemporal occurrence of such sites is limited in many types of terrestrial environments.
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20
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Mann EE, Wozniak DJ. Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 2012; 36:893-916. [PMID: 22212072 DOI: 10.1111/j.1574-6976.2011.00322.x] [Citation(s) in RCA: 378] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/18/2011] [Accepted: 12/19/2011] [Indexed: 11/27/2022] Open
Abstract
Biofilms are a predominant form of growth for bacteria in the environment and in the clinic. Critical for biofilm development are adherence, proliferation, and dispersion phases. Each of these stages includes reinforcement by, or modulation of, the extracellular matrix. Pseudomonas aeruginosa has been a model organism for the study of biofilm formation. Additionally, other Pseudomonas species utilize biofilm formation during plant colonization and environmental persistence. Pseudomonads produce several biofilm matrix molecules, including polysaccharides, nucleic acids, and proteins. Accessory matrix components shown to aid biofilm formation and adaptability under varying conditions are also produced by pseudomonads. Adaptation facilitated by biofilm formation allows for selection of genetic variants with unique and distinguishable colony morphology. Examples include rugose small-colony variants and wrinkly spreaders (WS), which over produce Psl/Pel or cellulose, respectively, and mucoid bacteria that over produce alginate. The well-documented emergence of these variants suggests that pseudomonads take advantage of matrix-building subpopulations conferring specific benefits for the entire population. This review will focus on various polysaccharides as well as additional Pseudomonas biofilm matrix components. Discussions will center on structure-function relationships, regulation, and the role of individual matrix molecules in niche biology.
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Affiliation(s)
- Ethan E Mann
- Department of Microbial Infection and Immunity, Department of Microbiology, Center for Microbial Interface Biology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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21
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Centler F, Fetzer I, Thullner M. Modeling population patterns of chemotactic bacteria in homogeneous porous media. J Theor Biol 2011; 287:82-91. [PMID: 21824482 DOI: 10.1016/j.jtbi.2011.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 07/22/2011] [Accepted: 07/26/2011] [Indexed: 10/17/2022]
Abstract
The spatio-temporal distribution of subsurface microorganisms determines their efficiency in providing essential ecosystem services such as the degradation of organic matter, the remineralization of carbon and nitrogen, or the remediation of anthropogenic contaminants. Populations of motile, chemotactic bacteria have been shown to be capable of pattern formation even in the absence of environmental heterogeneities. Focusing on the water saturated domain of the subsurface (e.g., aquatic sediments, porous aquifers), we analyze this innate capability of bacterial populations in an idealized model of a homogeneous, saturated porous medium. Considering a linear array of connected, identical microhabitats populated by motile, chemotactic bacterial cells, we identify prerequisites for pattern formation, analyze types of patterns, and assess their impact on substrate utilization. In our model, substrate supplied to the microhabitats facilitates bacterial growth, and microbial cells can migrate between neighboring microhabitats due to (i) random motility, (ii) chemotaxis towards substrate, and (iii) self-attraction. A precondition for inhomogeneous population patterns is analytically derived, stating that patterns are possible if the self-attraction exceeds a threshold defined by the random motility and the steady state population density in the microhabitats. An individual-based implementation of the model shows that static and dynamic population patterns can unfold. Degradation efficiency is highest for homogeneous bacterial distributions and decreases as pattern formation commences. If during biostimulation efforts the carrying capacity of the microhabitats is successively increased, simulation results show that degradation efficiency can unexpectedly decrease when the pattern formation threshold is crossed.
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Affiliation(s)
- Florian Centler
- Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany.
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22
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Hanzel J, Thullner M, Harms H, Wick LY. Microbial growth with vapor-phase substrate. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:858-864. [PMID: 21277662 DOI: 10.1016/j.envpol.2010.12.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 12/22/2010] [Accepted: 12/28/2010] [Indexed: 05/30/2023]
Abstract
Limited information exists on influences of the diffusive transport of volatile organic contaminants (VOC) on bacterial activity in the unsaturated zone of the terrestrial subsurface. Diffusion of VOC in the vapor-phase is much more efficient than in water and results in effective VOC transport and high bioavailability despite restricted mobility of bacteria in the vadose zone. Since many bacteria tend to accumulate at solid-water, solid-air and air-water interfaces, such phase boundaries are of a special interest for VOC-biodegradation. In an attempt to evaluate microbial activity toward air-borne substrates, this study investigated the spatio-temporal interplay between growth of Pseudomonas putida (NAH7) on vapor-phase naphthalene (NAPH) and its repercussion on vapor-phase NAPH concentrations. Our data demonstrate that growth rates of strain PpG7 were inversely correlated to the distance from the source of vapor-phase NAPH. Despite the high gas phase diffusivity of NAPH, microbial growth was absent at distances above 5 cm from the source when sufficient biomass was located in between. This indicates a high efficiency of suspended bacteria to acquire vapor-phase compounds and influence headspace concentration gradients at the centimeter-scale. It further suggests a crucial role of microorganisms as biofilters for gas-phase VOC emanating from contaminated groundwater or soil.
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Affiliation(s)
- Joanna Hanzel
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Germany
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23
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Caliz J, Vila X, Martí E, Sierra J, Nordgren J, Lindgren PE, Bañeras L, Montserrat G. The microbiota of an unpolluted calcareous soil faces up chlorophenols: Evidences of resistant strains with potential for bioremediation. CHEMOSPHERE 2011; 83:104-116. [PMID: 21295817 DOI: 10.1016/j.chemosphere.2011.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/21/2010] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
To highlight the effects of a variety of chlorophenols (CP) in relation to the response of an indigenous bacterial community, an agricultural Mediterranean calcareous soil has been studied in microcosms incubated under controlled laboratory conditions. Soil samples were artificially polluted with 2-monochlorophenol (MCP), 2,4,6-trichlorophenol (TCP) and pentachlorophenol (PCP), at concentrations ranging from 0.1 up to 5000 mg kg(-1). Both activity and composition of the microbial community were assessed during several weeks, respectively, by respirometric methods and PCR-DGGE analysis of extracted DNA and RNA. Significant decreases in soil respirometric values and changes in the bacterial community composition were observed at concentrations above 1000 mg kg(-1) MCP and TCP, and above 100 mg kg(-1) PCP. However, the persistence of several active bacterial populations in soil microcosms contaminated with high concentration of CP, as indicated by DGGE fingerprints, suggested the capacity of these native bacteria to survive in the presence of the pollutants, even without a previous adaptation or contact with them. The isolation of potential CP degraders was attempted by culture plating from microcosms incubated with high CP concentrations. Twenty-three different isolates were screened for their resistance to TCP and PCP. The most resistant isolates were identified as Kocuria palustris, Lysobacter gummosus, Bacillus sp. and Pseudomonas putida, according to 16S rRNA gene homology. In addition, these four isolates also showed the capacity to reduce the concentration of TCP and PCP from 15% to 30% after 5d of incubation in laboratory assays (initial pollutant concentration of 50 mg L(-1)). Isolate ITP29, which could be a novel species of Bacillus, has been revealed as the first known member in this bacterial group with potential for CP bioremediation applications, usually wide-spread in the soil natural communities, which has not been reported to date as a CP degrader.
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Affiliation(s)
- Joan Caliz
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Avda Montilivi s/n, Girona, Spain
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24
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Owsianiak M, Dechesne A, Binning PJ, Chambon JC, Sørensen SR, Smets BF. Evaluation of bioaugmentation with entrapped degrading cells as a soil remediation technology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:7622-7627. [PMID: 20812719 DOI: 10.1021/es101160u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Soil augmentation with microbial degraders immobilized on carriers is evaluated as a potential remediation technology using a mathematical model that includes degradation within spatially distributed carriers and diffusion or advection-dispersion as contaminant mass transfer mechanisms. The total volume of carriers is a critical parameter affecting biodegradation performance. In the absence of advection, 320 and 20 000 days are required to mineralize 90% of the herbicide linuron by Variovorax sp. SRS16 encapsulated in 2 mm beads with 5 and 20 mm spacings, respectively. Given that many pesticide degraders have low intrinsic degradation rates and that only limited carrier to soil volume ratios are practically feasible, bioaugmented soils are characterized by low effective degradation rates and can be considered fully mixed. A simple exponential model is then sufficient to predict biodegradation as verified by comparisons with published experimental data. By contrast, the full spatially distributed model is needed to adequately model the degradation of faster degrading contaminants such as naphthalene and benzene which can be mass-transfer limited. Dimensionless Damköhler numbers are proposed to determine whether the spatially distributed model is required. Results show that field scale applications of immobilized degraders will be limited by the amount of carriers required to reach acceptable degradation rates.
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Affiliation(s)
- Mikołaj Owsianiak
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Building 113, DK-2800 Kgs Lyngby, Denmark
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