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Relationship between Soil Fungi and Seedling Density in the Vicinity of Adult Conspecifics in an Arid Desert Forest. FORESTS 2021. [DOI: 10.3390/f12010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Research Highlights: 1. Soil fungi have a higher influence on seedling density compared to soil environmental factors; 2. Host-specific pathogens and beneficial fungi affect seeding density via different influencing mechanisms. Background and Objectives: The growth and development of seedlings are the key processes that affect forest regeneration and maintain community dynamics. However, the influencing factors of seedling growth around their adult conspecifics are not clear in arid desert forests. Probing the intrinsic relations among soil fungi, soil environmental factors (pH, water content, salinity, and nutrition), and seedling density will improve our understanding of forest development and provide a theoretical basis for forest management and protection. Materials and Methods: Four experimental plot types, depending on the distance to adult conspecifics, were set in an arid desert forest. Soil environmental factors, the diversity and composition of the soil fungal community, and the seedlings’ density and height were measured in the four experimental plot types, and their mutual relations were analyzed. Results: Seedling density as well as the diversity and composition of the soil fungal community varied significantly among the four plot types (p < 0.05). Soil environmental factors, especially soil salinity, pH, and soil water content, had significant influences on the seedling density and diversity and composition of the soil fungal community. The contribution of soil fungi (72.61%) to the variation in seedling density was much higher than the soil environmental factors (27.39%). The contribution of detrimental fungi to the variation in seedling density was higher than the beneficial fungi. Conclusions: Soil fungi mostly affected the distribution of seedling density in the vicinity of adult conspecifics in an arid desert forest. The distribution of seedling density in the vicinity of adults was mainly influenced by the detrimental fungi, while the adults in the periphery area was mainly influenced by the beneficial fungi.
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2
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Zhu B, Li C, Wang J, Li J, Li X. Elevation rather than season determines the assembly and co-occurrence patterns of soil bacterial communities in forest ecosystems of Mount Gongga. Appl Microbiol Biotechnol 2020; 104:7589-7602. [PMID: 32686007 DOI: 10.1007/s00253-020-10783-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 01/27/2023]
Abstract
Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community. KEY POINTS: • Seasonal dynamics of soil bacterial communities were studied in Mount Gongga. • The bacterial community was mainly affected by elevation rather than season. • Deterministic processes dominated bacterial community assembly. • The bacterial network was more complex but less stable at EBF than at DCF.
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Affiliation(s)
- Bingjian Zhu
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junming Wang
- Section of Climate Science, Illinois State Water Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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3
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Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation. Appl Environ Microbiol 2020; 86:AEM.01984-19. [PMID: 31732575 DOI: 10.1128/aem.01984-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/10/2019] [Indexed: 11/20/2022] Open
Abstract
As the range of bark beetles expands into new forests and woodlands, the need to understand their effects on multiple trophic levels becomes increasingly important. To date, much attention has been paid to the aboveground processes affected by bark beetle infestation, with a focus on photoautotrophs and ecosystem level processes. However, indirect effects of bark beetle on belowground processes, especially the structure and function of soil microbiota remains largely a black box. Our study examined the impacts of bark beetle-induced tree mortality on soil microbial community structure and function using high-throughput sequencing of the soil bacterial and fungal communities and measurements of extracellular enzyme activities. The results suggest bark beetle infestation affected edaphic conditions through increased soil water content, pH, electrical conductivity, and carbon/nitrogen ratio and altered bulk and rhizosphere soil microbial community structure and function. Finally, increased enzymatic activity suggests heightened microbial decomposition following bark beetle infestation. With this increase in enzymatic activity, nutrients trapped in organic substrates may become accessible to seedlings and potentially alter the trajectory of forest regeneration. Our results indicate the need for incorporation of microbial processes into ecosystem level models.IMPORTANCE Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle infestation. Our results show bark beetle infestation to impact soil conditions, as well as soil microbial community structure and function.
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4
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Rodríguez J, González-Pérez JA, Turmero A, Hernández M, Ball AS, González-Vila FJ, Arias ME. Physico-chemical and microbial perturbations of Andalusian pine forest soils following a wildfire. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:650-660. [PMID: 29642047 DOI: 10.1016/j.scitotenv.2018.04.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/19/2018] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Wildfires are a recurrent disturbance in Mediterranean forests, triggered by high fuel load, high environmental temperature and low humidity. Although, human intervention is behind the initiation of most fire episodes, the situation is likely to worsen in the future due to the effects of climate change in the Mediterranean "hot-spot". Here we study chemical, physical and microbial characteristics of burnt soils from two well differentiated sites at Sierra de Cazorla, Segura and Las Villas Natural Park, Andalusia, (Spain) affected and unaffected by a wildfire, and followed their evolution for three years. The soils affected by a severe surface burn showed a significant increase in organic matter after 3years from the fire. Viable bacteria and fungi also increased, especially 2-3years post-burning. Substrate induced respiration (SIR) also increased significantly in burnt soil from site 1 (rendzina on carbonate) while a significant decrease was observed in the burnt soils sampled from site 2 (calcic luvisols) in samples taken one month after the wildfire. A recovery in both SIR and organic matter was observed after 2 and 3years. Of seven soil enzymes studied, only phosphatase activity was significantly higher in most burnt soils over the three years. Analysis of bacterial community diversity using clone libraries showed a recovery in the number of phyla in burnt soils after 2 and 3years in both sites, with an increase in Proteobacteria and Firmicutes and a decrease in Acidobacteria phyla. For Bacteroidetes, the percentages were lower in most burnt samples. This study reveals that if wildfire increases the organic matter availability, then the microbial community responds with increased activity and biomass production. Although fire exerts an initial impact on the soil bacterial community, its structure and functional profile soon recovers (after 2-3years) contributing to soil recovery.
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Affiliation(s)
- Juana Rodríguez
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - José A González-Pérez
- Grupo de Materia orgánica en Suelos y Sedimentos (MOSS), Instituto de Recursos Naturales y Agrobiología (IRNAS-CSIC), Avda. Reina Mercedes, 10, 41012 Sevilla, Spain.
| | - Adriana Turmero
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - Manuel Hernández
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Francisco J González-Vila
- Grupo de Materia orgánica en Suelos y Sedimentos (MOSS), Instituto de Recursos Naturales y Agrobiología (IRNAS-CSIC), Avda. Reina Mercedes, 10, 41012 Sevilla, Spain
| | - M Enriqueta Arias
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá, 28805, Alcalá de Henares, Madrid, Spain
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5
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The Abundance of Fungi, Bacteria and Denitrification Genes during Insect Outbreaks in Scots Pine Forests. FORESTS 2018. [DOI: 10.3390/f9080497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Outbreaks of defoliating insects may affect microbial populations in forests and thereby mass balances and ecosystem functioning. Here, we investigated the microbial dynamics in Scots pine (Pinus sylvestris L.) forests during outbreaks of the nun moth (Lymantria monacha L.) and the pine-tree lappet (Dendrolimus pini L.). We used real-time PCR (polymerase chain reaction) to quantify genes that characterize bacterial and fungal abundance and the denitrification processes (nirK, nirS, nosZ clades I and II) in different forest compartments and we analyzed the C and N content of pine needles, insect feces, larvae, vegetation layers, organic layers, and mineral soil horizons. The infestation of the nun moth increased the bacterial abundance on pine needles, in the vegetation layer, and in the upper organic layer, while fungal populations were increased in the vegetation layer and upper organic layer during both outbreaks. In soil, the abundance of nirK increased after insect defoliation, while the C/N ratios decreased. nosZ clades I and II showed variable responses in different soil layers and to different defoliating insects. Our results illustrate changes in the microbial populations in pine forests that were infested by defoliating insects and changes in the chemical soil properties that foster these populations, indicating a genetic potential for increased soil N2O emissions during the defoliation peak of insect outbreak events.
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6
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Evidence of Ash Tree (Fraxinus spp.) Specific Associations with Soil Bacterial Community Structure and Functional Capacity. FORESTS 2018. [DOI: 10.3390/f9040187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Disturbance Alters the Relative Importance of Topographic and Biogeochemical Controls on Microbial Activity in Temperate Montane Forests. FORESTS 2018. [DOI: 10.3390/f9020097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest. mBio 2017; 8:mBio.01305-17. [PMID: 29208740 PMCID: PMC5717385 DOI: 10.1128/mbio.01305-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4+ concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.
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9
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Changes of Scots Pine Phyllosphere and Soil Fungal Communities during Outbreaks of Defoliating Insects. FORESTS 2017. [DOI: 10.3390/f8090316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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10
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Berlemont R, Martiny AC. Glycoside Hydrolases across Environmental Microbial Communities. PLoS Comput Biol 2016; 12:e1005300. [PMID: 27992426 PMCID: PMC5218504 DOI: 10.1371/journal.pcbi.1005300] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 01/06/2017] [Accepted: 12/11/2016] [Indexed: 11/25/2022] Open
Abstract
Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.
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Affiliation(s)
- Renaud Berlemont
- Dept. of Biological Sciences, California State University, Long Beach, California, United States of America
| | - Adam C. Martiny
- Dept. of Earth System Science, University of California, Irvine, California, United States of America
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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11
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Ferrenberg S, Martinez AS, Faist AM. Aboveground and belowground arthropods experience different relative influences of stochastic versus deterministic community assembly processes following disturbance. PeerJ 2016; 4:e2545. [PMID: 27761333 PMCID: PMC5068348 DOI: 10.7717/peerj.2545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/08/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces. METHODS Using a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies abundance, diversity, and composition. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models comparing observed vs. expected levels of species turnover (Beta diversity) among samples. RESULTS Tree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors. DISCUSSION Our results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a spatially co-occurring ground-dwelling arthropod community following disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of stochastic and deterministic processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory and considering conservation strategies.
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Affiliation(s)
- Scott Ferrenberg
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
| | - Alexander S. Martinez
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Akasha M. Faist
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, United States
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12
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Rare taxa maintain microbial diversity and contribute to terrestrial community dynamics throughout bark beetle infestation. Appl Environ Microbiol 2016; 82:6912-6919. [PMID: 27637881 DOI: 10.1128/aem.02245-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A global phenomenon of increasing bark beetle-induced tree mortality has heightened concern regarding ecosystem response and biogeochemical implications. Here we explore microbial dynamics under lodgepole pines through the analysis of bulk (16S rDNA) and potentially active (16S rRNA) communities to understand terrestrial ecosystem responses associated with this form of large-scale tree morality. We found that the relative abundance of bulk and potentially active taxa was correlated across taxonomic levels, but at lower levels cladal differences became more apparent. Despite this correlation, there was a strong differentiation of community composition between bulk and potentially active taxa, with further clustering in association with stages of tree mortality. Surprisingly, community clustering as a function of tree phase had limited correlation to soil water content and total nitrogen concentrations, which were the only two measured edaphic parameters to differ in association with tree phase. Bacterial clustering is more readily explained by the observed decrease in abundance of active, rare microorganisms after tree death in conjunction with stable alpha diversity measurements. This enables the rare fraction of the terrestrial microbial community to maintain metabolic diversity by transitioning between metabolically active and dormant states during this ecosystem disturbance and contributes disproportionately to community dynamics and archived metabolic capabilities. These results suggest that analyzing the bulk and potentially active communities after beetle infestation might be a more sensitive indicator of disruption than measuring local edaphic parameters. IMPORTANCE Forests around the world are experiencing unprecedented mortality due to insect infestations fueled in part by a changing climate. While above-ground processes have been explored, changes at the terrestrial interface relevant to microbial biogeochemical cycling remain largely unknown. In this study, we investigated the changing bulk and potentially active microbial communities beneath healthy and beetle-killed trees. We found that even though few edaphic parameters were altered from beetle infestation, the rare microbes were more likely to be active and fluctuate between dormancy and metabolic activity. This indicates rare as opposed to abundant taxa contribute disproportionately to microbial community dynamics and presumably biogeochemical cycling within these types of perturbed ecosystems.
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Nemergut DR, Knelman JE, Ferrenberg S, Bilinski T, Melbourne B, Jiang L, Violle C, Darcy JL, Prest T, Schmidt SK, Townsend AR. Decreases in average bacterial community rRNA operon copy number during succession. ISME JOURNAL 2015; 10:1147-56. [PMID: 26565722 PMCID: PMC5029226 DOI: 10.1038/ismej.2015.191] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 07/27/2015] [Accepted: 09/25/2015] [Indexed: 02/01/2023]
Abstract
Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
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Affiliation(s)
- Diana R Nemergut
- Department of Biology, Duke University, Durham, NC, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - Joseph E Knelman
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Scott Ferrenberg
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.,U.S. Geological Survey, Canyonlands Research Station, Moab, UT, USA
| | - Teresa Bilinski
- Department of Biological Sciences, St Edward's University, Austin, TX, USA
| | - Brett Melbourne
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lin Jiang
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cyrille Violle
- Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Tiffany Prest
- Department of Biology, Duke University, Durham, NC, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Alan R Townsend
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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14
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Kaňa J, Tahovská K, Kopáček J, Šantrůčková H. Excess of Organic Carbon in Mountain Spruce Forest Soils after Bark Beetle Outbreak Altered Microbial N Transformations and Mitigated N-Saturation. PLoS One 2015; 10:e0134165. [PMID: 26230678 PMCID: PMC4521819 DOI: 10.1371/journal.pone.0134165] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/06/2015] [Indexed: 11/19/2022] Open
Abstract
Mountain forests in National park Bohemian Forest (Czech Republic) were affected by bark beetle attack and windthrows in 2004-2008, followed by an extensive tree dieback. We evaluated changes in the biochemistry of the uppermost soil horizons with the emphasis on carbon (C) and nitrogen (N) cycling in a near-natural spruce (Picea abies) mountain forest after the forest dieback, and compared it with an undisturbed control plot of similar age, climate, elevation, deposition, N-saturation level, and land use history. We hypothesised that the high litter input after forest dieback at the disturbed plot and its consequent decomposition might influence the availability of C for microorganisms, and consequently, N transformations in the soil. The concentrations of dissolved organic C (DOC) and N (DON) in soil water extracts rapidly increased at the disturbed plot for 3 yeas and then continually decreased. Net ammonification exhibited a similar trend as DOC and DON, indicating elevated mineralization. Despite the high ammonium concentrations found after the forest dieback (an increase from 0.5 mmol kg-1 to 2-3 mmol kg-1), net nitrification was stable and low during these 3 years. After the DOC depletion and decrease in microbial biomass 5 years after the forest dieback, net nitrification started to rise, and nitrate concentrations increased from 0.2-1 mmol kg-1 to 2-3 mmol kg-1. Our results emphasize the key role of the availability of organic C in microbial N transformations, which probably promoted microbial heterotrophic activity at the expense of slow-growing nitrifiers.
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Affiliation(s)
- Jiří Kaňa
- Institute of Hydrobiology, Biology Centre of the CAS, v.v.i., České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
- * E-mail:
| | - Karolina Tahovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Jiří Kopáček
- Institute of Hydrobiology, Biology Centre of the CAS, v.v.i., České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
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15
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Ferrenberg S, Knelman JE, Jones JM, Beals SC, Bowman WD, Nemergut DR. Soil bacterial community structure remains stable over a 5-year chronosequence of insect-induced tree mortality. Front Microbiol 2014; 5:681. [PMID: 25566204 PMCID: PMC4267275 DOI: 10.3389/fmicb.2014.00681] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/20/2014] [Indexed: 12/20/2022] Open
Abstract
Extensive tree mortality from insect epidemics has raised concern over possible effects on soil biogeochemical processes. Yet despite the importance of microbes in nutrient cycling, how soil bacterial communities respond to insect-induced tree mortality is largely unknown. We examined soil bacterial community structure (via 16S rRNA gene pyrosequencing) and community assembly processes (via null deviation analysis) along a 5-year chronosequence (substituting space for time) of bark beetle-induced tree mortality in the southern Rocky Mountains, USA. We also measured microbial biomass and soil chemistry, and used in situ experiments to assess inorganic nitrogen mineralization rates. We found that bacterial community structure and assembly-which was strongly influenced by stochastic processes-were largely unaffected by tree mortality despite increased soil ammonium ([Formula: see text]) pools and reductions in soil nitrate ([Formula: see text]) pools and net nitrogen mineralization rates after tree mortality. Linear models suggested that microbial biomass and bacterial phylogenetic diversity are significantly correlated with nitrogen mineralization rates of this forested ecosystem. However, given the overall resistance of the bacterial community to disturbance from tree mortality, soil nitrogen processes likely remained relatively stable following tree mortality when considered at larger spatial and longer temporal scales-a supposition supported by the majority of available studies regarding biogeochemical effects of bark beetle infestations in this region. Our results suggest that soil bacterial community resistance to disturbance helps to explain the relatively weak effects of insect-induced tree mortality on soil N and C pools reported across the Rocky Mountains, USA.
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Affiliation(s)
- Scott Ferrenberg
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Joseph E. Knelman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
| | | | - Stower C. Beals
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
| | - William D. Bowman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
| | - Diana R. Nemergut
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
- Department of Biology, Duke UniversityDurham, NC, USA
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