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Shigyo N, Umeki K, Hirao T. Soil microbial identity explains home-field advantage for litter decomposition. THE NEW PHYTOLOGIST 2024. [PMID: 38736202 DOI: 10.1111/nph.19769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/25/2024] [Indexed: 05/14/2024]
Abstract
Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.
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Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
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2
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Dang C, Morrissey EM. The size and diversity of microbes determine carbon use efficiency in soil. Environ Microbiol 2024; 26:e16633. [PMID: 38733078 DOI: 10.1111/1462-2920.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.
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Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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Bosch J, Dobbler PT, Větrovský T, Tláskal V, Baldrian P, Brabcová V. Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda. FEMS Microbiol Ecol 2024; 100:fiae044. [PMID: 38640440 PMCID: PMC11030162 DOI: 10.1093/femsec/fiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.
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Affiliation(s)
- Jason Bosch
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Priscila Thiago Dobbler
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
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Faghihinia M, Halverson LJ, Hršelová H, Bukovská P, Rozmoš M, Kotianová M, Jansa J. Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus. Front Microbiol 2024; 14:1284648. [PMID: 38239731 PMCID: PMC10794670 DOI: 10.3389/fmicb.2023.1284648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood. Methods Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities. Results The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate. Conclusion Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.
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Affiliation(s)
- Maede Faghihinia
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Larry J. Halverson
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, United States
| | - Hana Hršelová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Petra Bukovská
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Martin Rozmoš
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Michala Kotianová
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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Li Y, Chen Z, Wagg C, Castellano MJ, Zhang N, Ding W. Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism. GLOBAL CHANGE BIOLOGY 2024; 30:e17101. [PMID: 38273560 DOI: 10.1111/gcb.17101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.
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Affiliation(s)
- Ye Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Cameron Wagg
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
| | | | - Nan Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Feng M, Varliero G, Qi W, Stierli B, Edwards A, Robinson S, van der Heijden MGA, Frey B. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environ Microbiol 2023; 25:3116-3138. [PMID: 37688461 DOI: 10.1111/1462-2920.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.
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Affiliation(s)
- Maomao Feng
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Serina Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil Interactions, Agroscope, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Wang S, Chen D, Liu Q, Zang L, Zhang G, Sui M, Dai Y, Zhou C, Li Y, Yang Y, Ding F. Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118889. [PMID: 37666128 DOI: 10.1016/j.jenvman.2023.118889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.
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Affiliation(s)
- Shasha Wang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Danmei Chen
- College of Forestry, Guizhou University, Guiyang, 550025, China.
| | - Qingfu Liu
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Lipeng Zang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Guangqi Zhang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Mingzhen Sui
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yu Dai
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Chunjie Zhou
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yujuan Li
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yousu Yang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Fangjun Ding
- Guizhou Libo Observation and Research Station for Karst Forest Ecosystem, National Forestry and Grassland Administration, Libo, 558400, China
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Barnett SE, Buckley DH. Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling. Environ Microbiol 2023; 25:1785-1795. [PMID: 37139849 DOI: 10.1111/1462-2920.16395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse 13 C-labelled carbon sources to soil and we used metagenomic-SIP to detect 13 C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a 13 C-labelled bacteriophage to its 13 C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were 13 C-labelled on Days 3-30, while 13 C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and 13 C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. These findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.
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Affiliation(s)
- Samuel E Barnett
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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Chen Y, Du Z, Weng ZH, Sun K, Zhang Y, Liu Q, Yang Y, Li Y, Wang Z, Luo Y, Gao B, Chen B, Pan Z, Van Zwieten L. Formation of soil organic carbon pool is regulated by the structure of dissolved organic matter and microbial carbon pump efficacy: A decadal study comparing different carbon management strategies. GLOBAL CHANGE BIOLOGY 2023; 29:5445-5459. [PMID: 37424182 DOI: 10.1111/gcb.16865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
To achieve long-term increases in soil organic carbon (SOC) storage, it is essential to understand the effects of carbon management strategies on SOC formation pathways, particularly through changes in microbial necromass carbon (MNC) and dissolved organic carbon (DOC). Using a 14-year field study, we demonstrate that both biochar and maize straw lifted the SOC ceiling, but through different pathways. Biochar, while raising SOC and DOC content, decreased substrate degradability by increasing carbon aromaticity. This resulted in suppressed microbial abundance and enzyme activity, which lowered soil respiration, weakened in vivo turnover and ex vivo modification for MNC production (i.e., low microbial carbon pump "efficacy"), and led to lower efficiency in decomposing MNC, ultimately resulting in the net accumulation of SOC and MNC. In contrast, straw incorporation increased the content and decreased the aromaticity of SOC and DOC. The enhanced SOC degradability and soil nutrient content, such as total nitrogen and total phosphorous, stimulated the microbial population and activity, thereby boosting soil respiration and enhancing microbial carbon pump "efficacy" for MNC production. The total C added to biochar and straw plots were estimated as 27.3-54.5 and 41.4 Mg C ha-1 , respectively. Our results demonstrated that biochar was more efficient in lifting the SOC stock via exogenous stable carbon input and MNC stabilization, although the latter showed low "efficacy". Meanwhile, straw incorporation significantly promoted net MNC accumulation but also stimulated SOC mineralization, resulting in a smaller increase in SOC content (by 50%) compared to biochar (by 53%-102%). The results address the decadal-scale effects of biochar and straw application on the formation of the stable organic carbon pool in soil, and understanding the causal mechanisms can allow field practices to maximize SOC content.
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Affiliation(s)
- Yalan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhangliu Du
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Zhe Han Weng
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ke Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yuqin Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Qin Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yan Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yang Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhibo Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yu Luo
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Bo Gao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Bin Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zezhen Pan
- Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Lukas Van Zwieten
- NSW Department of Primary Industries, Wollongbar Primary Industries Institute, Wollongbar, New South Wales, Australia
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Maillard F, Michaud TJ, See CR, DeLancey LC, Blazewicz SJ, Kimbrel JA, Pett-Ridge J, Kennedy PG. Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems 2023; 8:e0039023. [PMID: 37338274 PMCID: PMC10469842 DOI: 10.1128/msystems.00390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/21/2023] Open
Abstract
Microbial necromass contributes significantly to both soil carbon (C) persistence and ecosystem nitrogen (N) availability, but quantitative estimates of C and N movement from necromass into soils and decomposer communities are lacking. Additionally, while melanin is known to slow fungal necromass decomposition, how it influences microbial C and N acquisition as well as elemental release into soils remains unclear. Here, we tracked decomposition of isotopically labeled low and high melanin fungal necromass and measured 13C and 15N accumulation in surrounding soils and microbial communities over 77 d in a temperate forest in Minnesota, USA. Mass loss was significantly higher from low melanin necromass, corresponding with greater 13C and 15N soil inputs. A taxonomically and functionally diverse array of bacteria and fungi was enriched in 13C and/or 15N at all sampling points, with enrichment being consistently higher on low melanin necromass and earlier in decomposition. Similar patterns of preferential C and N enrichment of many bacterial and fungal genera early in decomposition suggest that both microbial groups co-contribute to the rapid assimilation of resource-rich soil organic matter inputs. While overall richness of taxa enriched in C was higher than in N for both bacteria and fungi, there was a significant positive relationship between C and N in co-enriched taxa. Collectively, our results demonstrate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate but also necromass C and N release and that both elements are rapidly co-utilized by diverse bacterial and fungal decomposers in natural settings. IMPORTANCE Recent studies indicate that microbial dead cells, particularly those of fungi, play an important role in long-term carbon persistence in soils. Despite this growing recognition, how the resources within dead fungal cells (also known as fungal necromass) move into decomposer communities and soils are poorly quantified, particularly in studies based in natural environments. In this study, we found that the contribution of fungal necromass to soil carbon and nitrogen availability was slowed by the amount of melanin present in fungal cell walls. Further, despite the overall rapid acquisition of carbon and nitrogen from necromass by a diverse range of both bacteria and fungi, melanization also slowed microbial uptake of both elements. Collectively, our results indicate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate, but also necromass carbon and nitrogen release into soil as well as microbial resource acquisition.
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Affiliation(s)
- François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Talia J. Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Craig R. See
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Peter G. Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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12
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Xiang D, Wang G, Tian J, Li W. Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments. Nat Commun 2023; 14:2171. [PMID: 37061518 PMCID: PMC10105724 DOI: 10.1038/s41467-023-37900-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Knowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (kref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and kref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and kref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.
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Affiliation(s)
- Daifeng Xiang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
| | - Gangsheng Wang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China.
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China.
| | - Jing Tian
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
| | - Wanyu Li
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, 430072, China
- Institute for Water-Carbon Cycles and Carbon Neutrality, School of Water Resources and Hydropower Engineering, Wuhan University, Wuhan, 430072, China
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13
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Teekaput C, Yasri S, Chaiwarith R. Cryptococcal Meningitis: Differences between Patients with and without HIV-Infection. Pathogens 2023; 12:pathogens12030427. [PMID: 36986349 PMCID: PMC10051108 DOI: 10.3390/pathogens12030427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Background: Cryptococcal meningitis is one of the most devastating infections, particularly in HIV-infected individuals. The increased use of immunosuppressants led to an increase in the incidence of cryptococcosis in HIV-uninfected individuals. This study aimed to compare the characteristics between groups. Methods: This retrospective cohort study was conducted from 2011 to 2021 in northern Thailand. Individuals diagnosed with cryptococcal meningitis aged ≥15 years were enrolled onto the study. Results: Out of 147 patients, 101 were individuals infected with HIV and 46 were non-infected. Factors associated with being infected with HIV included age < 45 years (OR 8.70, 95% CI 1.78–42.62), white blood cells < 5000 cells/cu.mm. (OR 7.18, 95% CI 1.45–35.61), and presence of fungemia (OR 5.86, 95% CI 1.17–42.62). Overall, the mortality rate was 24% (18% in HIV-infected vs. 37% in HIV-uninfected individuals, p-value = 0.020). Factors associated with mortality included concurrent pneumocystis pneumonia (HR 5.44, 95% CI 1.55–19.15), presence of alteration of consciousness (HR 2.94, 95% CI 1.42–6.10), infection caused by members of C. gattii species complex (HR 4.19, 95% CI 1.39–12.62), and anemia (HR 3.17, 95% CI 1.17–8.59). Conclusions: Clinical manifestations of cryptococcal meningitis differed between patients with and without HIV-infection in some aspects. Increasing awareness in physicians of this disease in HIV-uninfected individuals may prompt earlier diagnosis and timely treatment.
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Affiliation(s)
- Chutithep Teekaput
- Division of Neurology, Department of Internal Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saowaluck Yasri
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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14
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Kennedy PG, Maillard F. Knowns and unknowns of the soil fungal necrobiome. Trends Microbiol 2023; 31:173-180. [PMID: 36100506 DOI: 10.1016/j.tim.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 01/27/2023]
Abstract
Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.
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Affiliation(s)
- Peter G Kennedy
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - François Maillard
- Department of Plant & Microbiology, University of Minnesota, Saint Paul, MN 55108, USA
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15
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Štursová M, López-Mondéjar R, Baldrian P. Investigating the Bacterial and Fungal Communities Involved in Dead Biomass Degradation in Forest Soils. Methods Mol Biol 2022; 2605:157-168. [PMID: 36520393 DOI: 10.1007/978-1-0716-2871-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of microbial community members involved in a particular decomposition process. Further information can be gained (in SIP experiments) through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal and/or bacterial isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual microbial taxa. Here, we describe the use of these methods to explore the decomposer community of fungi and bacteria in forest litter and soil.
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Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Ruben López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic.
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16
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Zhang X, Huang Z, Zhong Z, Li Q, Bian F, Yang C. Metagenomic insights into the characteristics of soil microbial communities in the decomposing biomass of Moso bamboo forests under different management practices. Front Microbiol 2022; 13:1051721. [PMID: 36590390 PMCID: PMC9797724 DOI: 10.3389/fmicb.2022.1051721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Considering the rapid growth and high biomass productivity, Moso bamboo (Phyllostachys edulis) has high carbon (C) sequestration potential, and different management practices can strongly modify its C pools. Soil microorganisms play an important role in C turnover through dead plant and microbial biomass degradation. To date, little is known about how different management practices affect microbial carbohydrate-active enzymes (CAZymes) and their responses to dead biomass degradation. Methods Based on metagenomics analysis, this study analyzed CAZymes in three comparable stands from each Moso bamboo plantation: undisturbed (M0), extensively managed (M1), and intensively managed (M2). Results The results showed that the number of CAZymes encoding plant-derived component degradation was higher than that encoding microbe-derived component degradation. Compared with the M0, the CAZyme families encoding plant-derived cellulose were significantly (p < 0.05) high in M2 and significantly (p < 0.05) low in M1. For microbe-derived components, the abundance of CAZymes involved in the bacterial-derived peptidoglycan was higher than that in fungal-derived components (chitin and glucans). Furthermore, M2 significantly increased the fungal-derived chitin and bacterial-derived peptidoglycan compared to M0, whereas M1 significantly decreased the fungal-derived glucans and significantly increased the bacterial-derived peptidoglycan. Four bacterial phyla (Acidobacteria, Actinobacteria, Proteobacteria, and Chloroflexi) mainly contributed to the degradation of C sources from the plant and microbial biomass. Redundancy analysis (RDA) and mantel test suggested the abundance of CAZyme encoding genes for plant and microbial biomass degradation are significantly correlated with soil pH, total P, and available K. Least Squares Path Modeling (PLS-PM) showed that management practices indirectly affect the CAZyme encoding genes associated with plant and microbial biomass degradation by regulating the soil pH and nutrients (total N and P), respectively. Discussion Our study established that M2 and M1 impact dead biomass decomposition and C turnover, contributing to decreased C accumulation and establishing that the bacterial community plays the main role in C turnover in bamboo plantations.
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Affiliation(s)
- Xiaoping Zhang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China,Engineering Research Center of Biochar of Zhejiang Province, Zhejiang, China
| | - Zhiyuan Huang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Zheke Zhong
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China,*Correspondence: Zheke Zhong,
| | - Qiaoling Li
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Fangyuan Bian
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
| | - Chuanbao Yang
- Key Laboratory of Bamboo Forest Ecology and Resource Utilization of National Forestry and Grassland Administration, China National Bamboo Research Center, Zhejiang, China,National Long-term Observation and Research Station for Forest Ecosystem in Hangzhou-Jiaxing-Huzhou Plain, Zhejiang, China
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17
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Substrate and low intensity fires influence bacterial communities in longleaf pine savanna. Sci Rep 2022; 12:20904. [PMID: 36463255 PMCID: PMC9719495 DOI: 10.1038/s41598-022-24896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Bacterial communities associated with vegetation-soil interfaces have important roles in terrestrial ecosystems. These bacterial communities, studied almost exclusively in unburnt ecosystems or those affected by rare, high-intensity wildfires, have been understudied in fire-frequented grasslands and savannas. The composition of ground-level bacterial communities was explored in an old-growth pine savanna with a centuries-long management history of prescribed fires every 1-2 years. Using 16S metabarcoding, hypotheses were tested regarding differences in bacterial families of litter and soil surface substrates in patches of ground layer vegetation that were naturally burnt or unburnt during landscape-level prescribed fires. Litter/soil substrates and fire/no fire treatments explained 67.5% of bacterial community variation and differences, driven by relative abundance shifts of specific bacterial families. Fires did not strongly affect plant or soil variables, which were not linked to bacterial community differences. Litter/soil substrates and the naturally patchy frequent fires appear to generate microhabitat heterogeneity in this pine savanna, driving responses of bacterial families. Prescribed fire management may benefit from considering how fire-altered substrate heterogeneity influences and maintains microbial diversity and function, especially in these fiery ecosystems. Frequent, low-intensity fires appear ecologically important in maintaining the diverse microbial foundation that underlie ecosystem processes and services in fire-frequented habitats.
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18
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Sridhar B, Lawrence GB, Debenport SJ, Fahey TJ, Buckley DH, Wilhelm RC, Goodale CL. Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling. Environ Microbiol 2022; 24:6184-6199. [PMID: 35799501 DOI: 10.1111/1462-2920.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/28/2022] [Indexed: 01/12/2023]
Abstract
Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi (Cenococcum and Russula) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.
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Affiliation(s)
- Bhavya Sridhar
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Timothy J Fahey
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Christine L Goodale
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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19
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Yan Z, Kang E, Zhang K, Hao Y, Wang X, Li Y, Li M, Wu H, Zhang X, Yan L, Zhang W, Li J, Yang A, Niu Y, Kang X. Asynchronous responses of microbial CAZymes genes and the net CO 2 exchange in alpine peatland following 5 years of continuous extreme drought events. ISME COMMUNICATIONS 2022; 2:115. [PMID: 37938678 PMCID: PMC9723601 DOI: 10.1038/s43705-022-00200-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2023]
Abstract
Peatlands act as an important sink of carbon dioxide (CO2). Yet, they are highly sensitive to climate change, especially to extreme drought. The changes in the net ecosystem CO2 exchange (NEE) under extreme drought events, and the driving function of microbial enzymatic genes involved in soil organic matter (SOM) decomposition, are still unclear. Herein we investigated the effects of extreme drought events in different periods of plant growth season at Zoige peatland on NEE and microbial enzymatic genes of SOM decomposition after 5 years. The results showed that the NEE of peatland decreased significantly by 48% and 26% on average (n = 12, P < 0.05) under the early and midterm extreme drought, respectively. The microbial enzymatic genes abundance of SOM decomposition showed the same decreasing trend under early and midterm extreme drought, but an increasing trend under late extreme drought. The microbial community that contributes to these degradation genes mainly derives from Proteobacteria and Actinobacteria. NEE was mainly affected by soil hydrothermal factors and gross primary productivity but weakly correlated with SOM enzymatic decomposition genes. Soil microbial respiration showed a positive correlation with microbial enzymatic genes involved in the decomposition of labile carbon (n = 18, P < 0.05). This study provided new insights into the responses of the microbial decomposition potential of SOM and ecosystem CO2 sink function to extreme drought events in the alpine peatland.
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Affiliation(s)
- Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Enze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaodong Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Haidong Wu
- Information Center of Ministry of Ecology and Environment, 100029, Beijing, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Wantong Zhang
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China.
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China.
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China.
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20
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Mundra S, Kauserud H, Økland T, Nordbakken J, Ransedokken Y, Kjønaas OJ. Shift in tree species changes the belowground biota of boreal forests. THE NEW PHYTOLOGIST 2022; 234:2073-2087. [PMID: 35307841 PMCID: PMC9325058 DOI: 10.1111/nph.18109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The replacement of native birch with Norway spruce has been initiated in Norway to increase long-term carbon storage in forests. However, there is limited knowledge on the impacts that aboveground changes will have on the belowground microbiota. We examined which effects a tree species shift from birch to spruce stands has on belowground microbial communities, soil fungal biomass and relationships with vegetation biomass and soil organic carbon (SOC). Replacement of birch with spruce negatively influenced soil bacterial and fungal richness and strongly altered microbial community composition in the forest floor layer, most strikingly for fungi. Tree species-mediated variation in soil properties was a major factor explaining variation in bacterial communities. For fungi, both soil chemistry and understorey vegetation were important community structuring factors, particularly for ectomycorrhizal fungi. The relative abundance of ectomycorrhizal fungi and the ectomycorrhizal : saprotrophic fungal ratio were higher in spruce compared to birch stands, particularly in the deeper mineral soil layers, and vice versa for saprotrophs. The positive relationship between ergosterol (fungal biomass) and SOC stock in the forest floor layer suggests higher carbon sequestration potential in spruce forest soil, alternatively, that the larger carbon stock leads to an increase in soil fungal biomass.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
- Department of BiologyCollege of ScienceUnited Arab Emirates UniversityPO Box 15551Al‐Ain, Abu‐DhabiUnited Arab Emirates
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
| | - Tonje Økland
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
| | | | - Yngvild Ransedokken
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesPO Box 5003ÅsNO‐1432Norway
| | - O. Janne Kjønaas
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
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21
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. GLOBAL CHANGE BIOLOGY 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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22
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Wei Z, Ahmed Mohamed T, Zhao L, Zhu Z, Zhao Y, Wu J. Microhabitat drive microbial anabolism to promote carbon sequestration during composting. BIORESOURCE TECHNOLOGY 2022; 346:126577. [PMID: 34923079 DOI: 10.1016/j.biortech.2021.126577] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Transforming organic waste into stable carbon by composting is an eco-friendly way. However, the complex environment, huge microbial community and complicated metabolic of composting have limited the directional transformation of organic carbon, which is also not conducive to the fixation of organic carbon. Therefore, this review is based on the formation of humus, a stable by-product of composting, to expound how to promote carbon fixation by increasing the yield of humus. Firstly, we have clarified the transformation regularity of organic matter during composting. Meanwhile, the microhabitat factors affecting microbial catabolism and anabolism were deeply analyzed, in order to provide a theoretical basis for the micro habitat regulation of directional transformation of organic matter during composting. Given that, a method to adjust the directional humification and stabilization of organic carbon has been proposed. Hoping the rapid reduction and efficient stabilization of organic waste can be realized according to this method.
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Affiliation(s)
- Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Taha Ahmed Mohamed
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Soil, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
| | - Li Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zechen Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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23
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Baird A, Pope F. ‘Can't see the forest for the trees’: The importance of fungi in the context of UK tree planting. Food Energy Secur 2022. [DOI: 10.1002/fes3.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Aileen Baird
- School of Geography, Earth & Environmental Sciences Birmingham UK
- Birmingham Institute of Forest Research Birmingham UK
| | - Francis Pope
- School of Geography, Earth & Environmental Sciences Birmingham UK
- Birmingham Institute of Forest Research Birmingham UK
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24
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Bail J, Gomez JAM, de Oliveira Vaz GC, de Castro WAC, Bonugli-Santos RC. Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest. BMC Microbiol 2022; 22:10. [PMID: 34986801 PMCID: PMC8729104 DOI: 10.1186/s12866-021-02431-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis. RESULTS The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized. CONCLUSIONS Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.
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Affiliation(s)
- Jaqueline Bail
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Jose Alejandro Morales Gomez
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Wagner Antonio Chiba de Castro
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Rafaella Costa Bonugli-Santos
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil.
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25
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Bail J, Gomez JAM, de Oliveira Vaz GC, de Castro WAC, Bonugli-Santos RC. Structural and functional changes in the fungal community of plant detritus in an invaded Atlantic Forest. BMC Microbiol 2022. [PMID: 34986801 DOI: 10.1186/s12866-021-02431-859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Changes in the fungal community in the litter decomposition by invasive plants can negatively impact nutrient cycling in natural ecosystems. One still does not know the dimension of this hypothesis, but apparently, it is not despicable. This study evaluated the assemblage composition of fungi during litter decomposition in areas of Atlantic Forest invaded or not invaded by Tradescantia zebrina using Illumina MiSeq and metabarcoding analysis. RESULTS The invaded sample showed significantly higher richness and a difference in the species dominance than the invaded litter. Ascomycota was the first most abundant phylum in both areas. Even so, the dissimilarity between areas can be evidenced. The fungal from Basidiomycota were very representative in the non-invaded areas (ranged from an abundance of 43.29% in the non-invaded to 2.35% in the invaded sample). The genus Lepiota can indicate the primary functional group related to biomass degradation and showed the might difference about the invaded areas due to its essential reduction by the invader. In the invaded sample, there was a total absence of the endophyte-undefined saprotroph guild. Also, some genera not taxonomically characterized were eliminated in the invaded sample, revealing that the fungal biodiversity of areas has not yet been thoroughly characterized. CONCLUSIONS Hence, makes impossible the real interpretation of the invasive plant impact, showing the importance of continuing research on fungal biodiversity. It is important to emphasize that the replacement of the native species by T. zebrina may be responsible for the elimination of fungal groups that have not yet been identified.
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Affiliation(s)
- Jaqueline Bail
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Jose Alejandro Morales Gomez
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Wagner Antonio Chiba de Castro
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil
| | - Rafaella Costa Bonugli-Santos
- Federal University of Latin American Integration (UNILA), Institute Latin American of Nature and Life Sciences (ILACNV), Interdisciplinary Center of Life Sciences (CICV), 1000 Tarquínio Joslin dos Santos Av., Jardim Universitário, Foz do Iguaçu, PR, 85870-901, Brazil.
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26
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Malloch B, Kernaghan G, Walker AK. Temporal diversity patterns for fungi and mites associated with decaying Sporobolus pumilus ( Spartina patens) in the Minas Basin, Nova Scotia. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Coastal salt marshes provide many ecosystem services; however, little is known of the biology of decomposer taxa in these systems. This study employed aboveground and belowground litterbags to characterize the fungal and mite communities associated with the dominant salt marsh grass, Sporobolus pumilus, in the Minas Basin, Nova Scotia. Decomposition rates of aboveground and belowground tissues and environmental variables were quantified to contextualize temporal patterns in community composition. Aboveground litterbag mass loss peaked in July and decreased consistently over succeeding months, which positively correlated with fungal richness. Fungal and mite richness displayed inverse relationships over time, with mites gradually increasing in diversity before peaking in November, suggesting the presence of a complex detrital network where mites and fungi respond to different and possibly unrelated environmental cues. This study offers a first look at temporal community dynamics of two neglected groups of decomposers associated with S. pumilus in Canada.
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Affiliation(s)
- Bruce Malloch
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
- Department of Biology, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Gavin Kernaghan
- Department of Biology, Mount Saint Vincent University, Halifax, NS B3M 2J6, Canada
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
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27
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Lepinay C, Tláskal V, Vrška T, Brabcová V, Baldrian P. Successional development of wood-inhabiting fungi associated with dominant tree species in a natural temperate floodplain forest. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Differential Responses of Soil Bacterial and Fungal Community to Short-Term Crop Tree Management in a Larix gmelinii Plantation. FORESTS 2021. [DOI: 10.3390/f12101411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Crop tree management (CTM) is a widely applicable silviculture technology that is used to improve the performance of individual trees. However, only little information is available about the effects of the CTM regime on the soil microbial community structure. We conducted a study to explore the effects of short-term (five years) CTM on the soil bacterial and fungal diversity, community composition, and structure in the 0–10 cm soil layer in a Larix gmelinii (Rupr.) Kuzen. plantation. We set out to investigate the differential response of bacterial and fungal communities to variations in soil properties mediated by short-term CTM. Compared with the control plots, the soil microbial biomass carbon and microbial biomass nitrogen in CTM increased significantly by 64.2% and 32.3%, respectively. CTM significantly promoted the content of soil organic carbon, dissolved organic carbon, and nitrate nitrogen, and reduced the content of dissolved organic nitrogen. CTM changed the Shannon and Simpson indices of soil fungi to a remarkable extent but had little effect on the α diversity of bacterial communities. The bacterial β diversity was more sensitive to CTM than fungi. The relative abundance of Verrucomicrobiae (the dominant class of soil bacteria) in CTM was significantly increased by 78.2%, while the relative abundance of Agaricomycetes (dominant class for soil fungi) was reduced by 43.3%. We observed a significantly increased number of unique OTUs for soil fungi in the CTM plots. Redundancy analysis showed that dissolved organic carbon, soil moisture, and total phosphorus content significantly affected the composition of bacterial communities, while soil dissolved organic nitrogen, C/N, and total phosphorus drove the high variation in fungal community composition. Overall, our results emphasize the divergent response of soil bacterial and fungal communities in Larix gmelinii plantations to short-term CTM. We must pay more attention to the functional role of soil microbiota in future forest management.
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29
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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30
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Kroeger ME, Rae DeVan M, Thompson J, Johansen R, Gallegos-Graves LV, Lopez D, Runde A, Yoshida T, Munsky B, Sevanto S, Albright MBN, Dunbar J. Microbial community composition controls carbon flux across litter types in early phase of litter decomposition. Environ Microbiol 2021; 23:6676-6693. [PMID: 34390621 PMCID: PMC9291330 DOI: 10.1111/1462-2920.15705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022]
Abstract
Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non‐labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition.
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Affiliation(s)
- Marie E Kroeger
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - M Rae DeVan
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.,Manaaki Whenua - Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, New Zealand
| | | | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Andreas Runde
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Thomas Yoshida
- Chemical Diagnostics and Engineering, Los Alamos National Laboratory, Mailstop K484, Los Alamos, NM, 87544, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA.,School of Biomedical Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Mailstop J495, Los Alamos, NM, 87545, USA
| | - Michaeline B N Albright
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
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31
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Gorfer M, Mayer M, Berger H, Rewald B, Tallian C, Matthews B, Sandén H, Katzensteiner K, Godbold DL. High Fungal Diversity but Low Seasonal Dynamics and Ectomycorrhizal Abundance in a Mountain Beech Forest. MICROBIAL ECOLOGY 2021; 82:243-256. [PMID: 33755773 PMCID: PMC8282586 DOI: 10.1007/s00248-021-01736-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/10/2021] [Indexed: 05/05/2023]
Abstract
Forests on steep slopes constitute a significant proportion of European mountain areas and are important as production and protection forests. This study describes the soil fungal community structure in a European beech-dominated mountain forest stands in the Northern Calcareous Alps and investigates how it is determined by season and soil properties. Samples were collected at high spatial resolution in an area of ca. 100 m × 700 m in May (spring) and August (summer). Illumina MiSeq high-throughput sequencing of the ITS2-region revealed distinct patterns for the soil fungal communities. In contrast to other studies from temperate European beech forest stands, Ascomycota dominated the highly diverse fungal community, while ectomycorrhizal fungi were of lower abundance. Russulaceae, which are often among the dominant ectomycorrhizal fungi associated with European beech, were absent from all samples. Potentially plant pathogenic fungi were more prevalent than previously reported. Only subtle seasonal differences were found between fungal communities in spring and summer. Especially, dominant saprotrophic taxa were largely unaffected by season, while slightly stronger effects were observed for ectomycorrhizal fungi. Soil characteristics like pH and organic carbon content, on the other hand, strongly shaped abundant taxa among the saprotrophic fungal community.
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Affiliation(s)
- Markus Gorfer
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Mathias Mayer
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | | | - Boris Rewald
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria.
| | - Claudia Tallian
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Bradley Matthews
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
- Environment Agency Austria, Vienna, Austria
| | - Hans Sandén
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Klaus Katzensteiner
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
| | - Douglas L Godbold
- Forest Ecology, Dept. of Forest and Soil Sciences, University of Natural Resources and Life Sciences (BOKU), Peter-Jordan-Strasse 82, 1190, Vienna, Austria
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32
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Tláskal V, Baldrian P. Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition. Front Microbiol 2021; 12:685303. [PMID: 34220772 PMCID: PMC8247643 DOI: 10.3389/fmicb.2021.685303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.
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Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
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33
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Fungi and Circular Economy: Pleurotus ostreatus Grown on a Substrate with Agricultural Waste of Lavender, and Its Promising Biochemical Profile. RECYCLING 2021. [DOI: 10.3390/recycling6020040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The increasing production of essential oils has generated a significant amount of vegetal waste that must be discarded, increasing costs for farmers. In this context, fungi, due to their ability to recycle lignocellulosic matter, may be used to turn this waste into new products, thus generating additional income for essential oil producers. The objectives of our work, within the framework of the European ALCOTRA project FINNOVER, were two-fold. The first was to cultivate Pleurotus ostreatus on solid waste of lavender used for essential oil production. The second was to provide, at the same time, new products that can increase the income of small and medium farms in the Ligurian Italian Riviera. This paper presents two pilot tests in which P. ostreatus was grown on substrates with five different concentrations of lavender waste, ranging from 0 to 100% (w/w). Basidiomata grown on all the substrates and their biochemical profiles were characterized using high-performance liquid chromatography coupled to mass spectrometry. The biochemical analysis of mushrooms proved the presence of molecules with antioxidant and potential pharmacological properties, in particular in mushrooms grown on lavender-enriched substrates. The results open the possibility of producing mushrooms classified as a novel food. Furthermore, the results encourage further experiments aimed at investigating how different substrates positively affect the metabolomics of mushrooms.
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34
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Hu D, Baskin JM, Baskin CC, Liu R, Yang X, Huang Z. A Seed Mucilage-Degrading Fungus From the Rhizosphere Strengthens the Plant-Soil-Microbe Continuum and Potentially Regulates Root Nutrients of a Cold Desert Shrub. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:538-546. [PMID: 33596107 DOI: 10.1094/mpmi-01-21-0014-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seed mucilage plays important roles in the adaptation of desert plants to the stressful environment. Artemisia sphaerocephala is an important pioneer plant in the Central Asian cold desert, and it produces a large quantity of seed mucilage. Seed mucilage of A. sphaerocephala can be degraded by soil microbes, but it is unknown which microorganisms can degrade mucilage or how the mucilage-degrading microorganisms affect rhizosphere microbial communities or root nutrients. Here, mucilage-degrading microorganisms were isolated from the rhizosphere of A. sphaerocephala, were screened by incubation with mucilage stained with Congo red, and were identified by sequencing and phylogenetic analyses. Fungal-bacterial networks based on high-throughput sequencing of rhizosphere microbes were constructed to explore the seasonal dynamic of interactions between a mucilage-degrading microorganism and its closely related microorganisms. The structural equation model was used to analyze effects of the mucilage-degrading microorganism, rhizosphere fungal-bacterial communities, and soil physicochemical properties on root C and N. The fungus Phanerochaete chrysosporium was identified as a mucilage-degrading microorganism. Relative abundance of the mucilage-degrading fungus (MDF) was highest in May. Subnetworks showed that the abundance of fungi and bacteria closely related to the MDF also were highest in May. Interactions between the MDF and related fungi and bacteria were positive, which might enhance mucilage degradation. In addition, the MDF might regulate root C and N by affecting rhizosphere microbial community structure. Our results suggest that MDF from the rhizosphere strengthens the plant-soil-microbe continuum, thereby potentially regulating microbial interactions and root nutrients of A. sphaerocephala.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Dandan Hu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, U.S.A
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY 40506, U.S.A
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Rong Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xuejun Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhenying Huang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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35
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Netherway T, Bengtsson J, Krab EJ, Bahram M. Biotic interactions with mycorrhizal systems as extended nutrient acquisition strategies shaping forest soil communities and functions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil. Sci Rep 2021; 11:831. [PMID: 33437021 PMCID: PMC7804402 DOI: 10.1038/s41598-020-80840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.
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See CR, Fernandez CW, Conley AM, DeLancey LC, Heckman KA, Kennedy PG, Hobbie SE. Distinct carbon fractions drive a generalisable two‐pool model of fungal necromass decomposition. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Craig R. See
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Chris W. Fernandez
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Anna M. Conley
- Department of Chemistry Carleton College Northfield MN USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | | | - Peter G. Kennedy
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Sarah E. Hobbie
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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Štursová M, Kohout P, Human ZR, Baldrian P. Production of Fungal Mycelia in a Temperate Coniferous Forest Shows Distinct Seasonal Patterns. J Fungi (Basel) 2020; 6:E190. [PMID: 32993121 PMCID: PMC7712845 DOI: 10.3390/jof6040190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
In temperate forests, climate seasonality restricts the photosynthetic activity of primary producers to the warm season from spring to autumn, while the cold season with temperatures below the freezing point represents a period of strongly reduced plant activity. Although soil microorganisms are active all-year-round, their expressions show seasonal patterns. This is especially visible on the ectomycorrhizal fungi, the most abundant guild of fungi in coniferous forests. We quantified the production of fungal mycelia using ingrowth sandbags in the organic layer of soil in temperate coniferous forest and analysed the composition of fungal communities in four consecutive seasons. We show that fungal biomass production is as low as 0.029 µg g-1 of sand in December-March, while it reaches 0.122 µg g-1 in June-September. The majority of fungi show distinct patterns of seasonal mycelial production, with most ectomycorrhizal fungi colonising ingrowth bags in the spring or summer, while the autumn and winter colonisation was mostly due to moulds. Our results indicate that fungal taxa differ in their seasonal patterns of mycelial production. Although fungal biomass turnover appears all-year-round, its rates are much faster in the period of plant activity than in the cold season.
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Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
| | | | | | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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40
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Long-term decomposition of litter in the montane forest and the definition of fungal traits in the successional space. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100913] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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41
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Pent M, Bahram M, Põldmaa K. Fruitbody chemistry underlies the structure of endofungal bacterial communities across fungal guilds and phylogenetic groups. THE ISME JOURNAL 2020; 14:2131-2141. [PMID: 32409757 PMCID: PMC7368025 DOI: 10.1038/s41396-020-0674-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/06/2023]
Abstract
Eukaryote-associated microbiomes vary across host taxa and environments but the key factors underlying their diversity and structure in fungi are still poorly understood. Here we determined the structure of bacterial communities in fungal fruitbodies in relation to the main chemical characteristics in ectomycorrhizal (EcM) and saprotrophic (SAP) mushrooms as well as in the surrounding soil. Our analyses revealed significant differences in the structure of endofungal bacterial communities across fungal phylogenetic groups and to a lesser extent across fungal guilds. These variations could be partly ascribed to differences in fruitbody chemistry, particularly the carbon-to-nitrogen ratio and pH. Fungal fruitbodies appear to represent nutrient-rich islands that derive their microbiome largely from the underlying continuous soil environment, with a larger overlap of operational taxonomic units observed between SAP fruitbodies and the surrounding soil, compared with EcM fungi. In addition, bacterial taxa involved in the decomposition of organic material were relatively more abundant in SAP fruitbodies, whereas those involved in release of minerals were relatively more enriched in EcM fruitbodies. Such contrasts in patterns and underlying processes of the microbiome structure between SAP and EcM fungi provide further evidence that bacteria can support the functional roles of these fungi in terrestrial ecosystems.
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Affiliation(s)
- Mari Pent
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden.
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
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42
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Albright MBN, Thompson J, Kroeger ME, Johansen R, Ulrich DEM, Gallegos-Graves LV, Munsky B, Dunbar J. Differences in substrate use linked to divergent carbon flow during litter decomposition. FEMS Microbiol Ecol 2020; 96:5867763. [DOI: 10.1093/femsec/fiaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
ABSTRACT
Discovering widespread microbial processes that create variation in soil carbon (C) cycling within ecosystems may improve soil C modeling. Toward this end, we screened 206 soil communities decomposing plant litter in a common garden microcosm environment and examined features linked to divergent patterns of C flow. C flow was measured as carbon dioxide (CO2) and dissolved organic carbon (DOC) from 44-days of litter decomposition. Two large groups of microbial communities representing ‘high’ and ‘low’ DOC phenotypes from original soil and 44-day microcosm samples were down-selected for fungal and bacterial profiling. Metatranscriptomes were also sequenced from a smaller subset of communities in each group. The two groups exhibited differences in average rate of CO2 production, demonstrating that the divergent patterns of C flow arose from innate functional constraints on C metabolism, not a time-dependent artefact. To infer functional constraints, we identified features – traits at the organism, pathway or gene level – linked to the high and low DOC phenotypes using RNA-Seq approaches and machine learning approaches. Substrate use differed across the high and low DOC phenotypes. Additional features suggested that divergent patterns of C flow may be driven in part by differences in organism interactions that affect DOC abundance directly or indirectly by controlling community structure.
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Affiliation(s)
- Michaeline B N Albright
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Marie E Kroeger
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Renee Johansen
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | - Danielle E M Ulrich
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
| | | | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA
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Xiao L, Zhang C, Wang G, Guan D, Zhang R, Chen Y, Dai J. Influencing pathways of soil microbial attributes on accumulation of heavy metals in brassica (Brassica campestris L. ssp.chinensis var.utilis Tsen et Lee) leaves. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114215. [PMID: 32142975 DOI: 10.1016/j.envpol.2020.114215] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 02/11/2020] [Accepted: 02/16/2020] [Indexed: 05/22/2023]
Abstract
Microbial attributes have a great impact on soil heavy metal bioavailability, yet their influencing pathway on heavy metal accumulation in crop plants remains elusive. This study was aimed to analyze the influencing pathways of microbial attributes, including microbial biomass C and N (MBC and MBN), basal soil respiration (BSR) along with the activities of catalase, urease, and sucrase, on heavy metals (i.e., Cd, Cr, Cu, Ni, Pb, and Zn) accumulation by brassica leaves. Based upon a field investigation close to electroplating factory outlets, 45 pairs of soil and brassica samples were analyzed in the laboratory. Concentrations of heavy metals in brassica leaves declined with sampling distances downstream from the outlets. Redundancy analysis indicated that bioavailable concentrations of Cr, Cu, Ni, and MBC along with catalase activity were the major variables influencing heavy metal accumulation in brassica leaves and accounted for 83% of the accumulation. MBC and catalase activity accounted for 17% of the heavy metal accumulation in brassica leaves. Stepwise regression indicated that catalase activity, MBC, and BSR significantly affected heavy metal accumulation in brassica leaves. Based on structural equation modeling, the pathway coefficient of microbial activities-brassica heavy metals and the pathway coefficient of microbial biomass-brassica heavy metals are 0.122 (P < 0.05), suggesting that these microbial attributes (i.e. MBC along with catalase activities and SBR) could affect heavy metal accumulation in brassica leaves directly. The pathway coefficients of microbial activities-bioavailable heavy metals-brassica heavy metals and microbial biomass-bioavailable heavy metals-brassica heavy metal were -0.541 (P < 0.001) and 0.453 (P < 0.001), respectively, indicating that increase of microbial activities inhibited heavy metal accumulation while increase of microbial biomass promoted heavy metal accumulation, in brassica leaves. These results suggested that heavy metal bioavailability played a mediating role in the influencing pathways of soil microbial attributes on heavy metals in brassica leaves.
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Affiliation(s)
- Ling Xiao
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Chi Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Gang Wang
- School of Management, Guangdong University of Technology, Guangzhou, 510520, China
| | - Dongsheng Guan
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Renduo Zhang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yujuan Chen
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jun Dai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
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44
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Montes de Oca-Vásquez G, Solano-Campos F, Vega-Baudrit JR, López-Mondéjar R, Odriozola I, Vera A, Moreno JL, Bastida F. Environmentally relevant concentrations of silver nanoparticles diminish soil microbial biomass but do not alter enzyme activities or microbial diversity. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122224. [PMID: 32058228 DOI: 10.1016/j.jhazmat.2020.122224] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/03/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
The increasing use of silver nanoparticles (AgNPs) due to their well-known antimicrobial activity, has led to their accumulation in soil ecosystems. However, the impact of environmental realistic concentrations of AgNPs on the soil microbial community has been scarcely studied. In this work, we have assessed the impact of AgNPs, that mimic real concentrations in nature, on tropical soils cultivated with Coffea arabica under conventional and organic management systems. We evaluated the biomass, extracellular enzyme activities, and diversity of the soil microbial community, in a microcosm experiment as a function of time. After seven days of incubation, we found an increase in microbial biomass in an AgNPs-concentration-independent manner. In contrast, after 60-day-incubation, there was a decrease in Gram+ and actinobacterial biomass, in both soils and all AgNPs concentrations. Soil physico-chemical properties and enzyme activities were not affected overall by AgNPs. Regarding the microbial community composition, only some differences in the relative abundance at phylum and genus level in the fungal community were observed. Our results suggest that environmental concentrations of AgNPs affected microbial biomass but had little impact on microbial diversity and may have little effects on the soil biogeochemical cycles mediated by extracellular enzyme activities.
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Affiliation(s)
- Gabriela Montes de Oca-Vásquez
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Costa Rica.
| | - Frank Solano-Campos
- School of Biological Sciences, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - José R Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Laboratory of Polymer Science and Technology, School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Alfonso Vera
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation, Campus Universitario de Espinardo, 30100, Murcia, Spain
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45
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Ryan ME, Schreiner KM, Swenson JT, Gagne J, Kennedy PG. Rapid changes in the chemical composition of degrading ectomycorrhizal fungal necromass. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Low A, Zhao S, Rogers MJ, Zemb O, Lee M, He J, Manefield M. Isolation, characterization and bioaugmentation of an acidotolerant 1,2-dichloroethane respiring Desulfitobacterium species from a low pH aquifer. FEMS Microbiol Ecol 2020; 95:5454739. [PMID: 30980656 DOI: 10.1093/femsec/fiz055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
A Desulfitobacterium sp. strain AusDCA of the Peptococcaceae family capable of respiring 1,2-dichloroethane (1,2-DCA) to ethene anaerobically with ethanol or hydrogen as electron donor at pH 5.0 with optimal range between pH 6.5-7.5 was isolated from an acidic aquifer near Sydney, Australia. Strain AusDCA is distant (94% nucleotide identity) from its nearest phylogenetic neighbor, D. metallireducens, and could represent a new species. Reference gene-based quantification of growth indicated a doubling time of 2 days in cultures buffered at pH 7.2, and a yield of 7.66 (± 4.0) × 106 cells µmol-1 of 1,2-DCA. A putative 1,2-DCA reductive dehalogenase was translated from a dcaAB locus and had high amino acid identity (97.3% for DcaA and 100% for DcaB) to RdhA1B1 of the 1,2-DCA respiring Dehalobacter strain WL. Proteomic analysis confirmed DcaA expression in the pure culture. Dehalogenation of 1,2-DCA (1.6 mM) was observed in batch cultures established from groundwater at pH 5.5 collected 38 days after in situ bioaugmentation but not in cultures established with groundwater collected at the same time from wells not receiving bioaugmentation. Overall, strain AusDCA can tolerate lower pH than previously characterized organohalide respiring bacteria and remained viable in groundwater at pH 5.5.
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Affiliation(s)
- Adrian Low
- Genome Structural Biology, Temasek Lifesciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Matthew Lee
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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47
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Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J. Niche differentiation is spatially and temporally regulated in the rhizosphere. THE ISME JOURNAL 2020; 14:999-1014. [PMID: 31953507 PMCID: PMC7082339 DOI: 10.1038/s41396-019-0582-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 10/28/2019] [Accepted: 12/18/2019] [Indexed: 01/14/2023]
Abstract
The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.
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Affiliation(s)
- Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Mary K Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
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48
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Maillard F, Schilling J, Andrews E, Schreiner KM, Kennedy P. Functional convergence in the decomposition of fungal necromass in soil and wood. FEMS Microbiol Ecol 2019; 96:5685958. [DOI: 10.1093/femsec/fiz209] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Understanding the post-senescent fate of fungal mycelium is critical to accurately quantifying forest carbon and nutrient cycling, but how this organic matter source decomposes in wood remains poorly studied. In this study, we compared the decomposition of dead fungal biomass (a.k.a. necromass) of two species, Mortierella elongata and Meliniomyces bicolor, in paired wood and soil plots in a boreal forest in northern Minnesota, USA. Mass loss was quantified at four time points over an 8-week incubation and the richness and composition of the fungal communities colonizing fungal necromass were characterized using high-throughput sequencing. We found that the structure of fungal decomposer communities in wood and soil differed, but, in both habitats, there was relatively rapid decay (∼30% remaining after 56 days). Mass loss was significantly faster in soil and for high-quality (i.e. high nitrogen and low melanin) fungal necromass. In both habitats, there was a clear trajectory of early colonization by opportunistic fungal taxa followed by colonization of fungi with greater enzymatic capacities to degrade more recalcitrant compounds, including white-rot and ectomycorrhizal fungi. Collectively, our results indicate that patterns emerging regarding substrate quality effects on fungal necromass decomposition in soil and leaf litter can be largely extended to fungal necromass decomposition in wood.
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Affiliation(s)
- François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Jonathan Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Erin Andrews
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Kathryn M Schreiner
- Department of Chemistry and Biochemistry, University of Minnesota, Dulut 55812, MN 55108, USA
- Large Lakes Observatory, University of Minnesota, Dulut 55812, MN 55108, USA
| | - Peter Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
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Zanne AE, Abarenkov K, Afkhami ME, Aguilar-Trigueros CA, Bates S, Bhatnagar JM, Busby PE, Christian N, Cornwell WK, Crowther TW, Flores-Moreno H, Floudas D, Gazis R, Hibbett D, Kennedy P, Lindner DL, Maynard DS, Milo AM, Nilsson RH, Powell J, Schildhauer M, Schilling J, Treseder KK. Fungal functional ecology: bringing a trait-based approach to plant-associated fungi. Biol Rev Camb Philos Soc 2019; 95:409-433. [PMID: 31763752 DOI: 10.1111/brv.12570] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/21/2022]
Abstract
Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun ). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.
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Affiliation(s)
- Amy E Zanne
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Kessy Abarenkov
- Natural History Museum, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, U.S.A
| | - Carlos A Aguilar-Trigueros
- Freie Universität-Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research, 14195, Berlin, Germany
| | - Scott Bates
- Department of Biological Sciences, Purdue University Northwest, Westville, IN, 46391, U.S.A
| | | | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, U.S.A
| | - Natalie Christian
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, U.S.A.,Department of Biology, University of Louisville, Louisville, KY 40208, U.S.A
| | - William K Cornwell
- Evolution & Ecology Research Centre, School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Habacuc Flores-Moreno
- Department of Ecology, Evolution, and Behavior, and Department of Forest Resources, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Dimitrios Floudas
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Romina Gazis
- Department of Plant Pathology, Tropical Research & Education Center, University of Florida, Homestead, FL, 33031, U.S.A
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, 01610, U.S.A
| | - Peter Kennedy
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, WI, 53726, U.S.A
| | - Daniel S Maynard
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Amy M Milo
- Department of Biological Sciences, George Washington University, Washington, DC, 20052, U.S.A
| | - Rolf Henrik Nilsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Box 461, 405 30, Göteborg, Sweden
| | - Jeff Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Mark Schildhauer
- National Center for Ecological Analysis and Synthesis, 735 State Street, Suite 300, Santa Barbara, CA, 93101, U.S.A
| | - Jonathan Schilling
- Plant & Microbial Biology, University of Minnesota, St. Paul, MN, 55108, U.S.A
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, U.S.A
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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