101
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Effect of Charcoal on the Properties, Enzyme Activities and Microbial Diversity of Temperate Pine Forest Soils. FORESTS 2021. [DOI: 10.3390/f12111488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Relict charcoal hearths (RCHs) increases soil fertility in forest ecosystems. However, the effects of RCHs on the activity and abundance of soil microorganisms remain unknown. In this paper, we analysed the impact of relict charcoal production on the soil enzymatic activity and composition of soil bacterial and fungal communities in Scots pine forests of the Manowo Forest District in northern Poland. Moreover, we determined the effect of relict charcoal production on the soil properties. Our research was conducted by comparing the physical, chemical, enzymatic and microbiological properties of charcoal-enriched and charcoal-free soils. Significant differences in physical properties were found between these two soil types in terms of their structure and water holding capacity. As expected, horizons enriched with charcoal were characterised by a significantly higher organic carbon content (4.7% on average compared to 2.2% in control horizons), and also by a considerably higher content of available phosphorus (an average of 64.07 mg·kg−1 compared to 36.21 mg·kg−1 in the control). Similarly, RCH horizons displayed a higher pH and higher contents of Ca and Na cations. These results indicated that RCH soils provided more favourable conditions for the soil microbiome, as reflected by the higher enzymatic activity and diversity of the microorganisms. Moreover, bacterial and fungal communities in RCH soils were more diverse and had greater species/genera richness, especially in the case of fungi. Members of the genus Rhodoplanes dominated the bacterial community at both RCH and non-RCH sites, followed by Streptomyces, Burkholderia, Skermanella, Tsukamurella and Candidatus Solibacter. Both culture- and next generation sequencing (NGS)-based analyses showed that soil fungal communities were dominated by Ascomycota, with Penicillium as the most abundant genus. Our results showed that hearth soils may represent a significant C pool in the forest ecosystem. This study supports the strategy of safeguarding such charcoal-enriched soils as precious C reservoirs and ecologically important biodiversity hotspots. Moreover, the application of charcoal may effectively increase the microbial diversity of forest soils, especially during the reforestation or re-cultivation of disturbed habitats.
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102
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Abstract
Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.
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103
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Sawada K, Watanabe S, Nguyen HL, Sugihara S, Seki M, Kobayashi H, Toyota K, Funakawa S. Comparison of the Structure and Diversity of Root-Associated and Soil Microbial Communities Between Acacia Plantations and Native Tropical Mountain Forests. Front Microbiol 2021; 12:735121. [PMID: 34659163 PMCID: PMC8511777 DOI: 10.3389/fmicb.2021.735121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/18/2021] [Indexed: 12/03/2022] Open
Abstract
Deforestation of native tropical forests has occurred extensively over several decades. The plantation of fast-growing trees, such as Acacia spp., is expanding rapidly in tropical regions, which can contribute to conserve the remaining native tropical forests. To better understand belowground biogeochemical cycles and the sustainable productivity of acacia plantations, we assessed the effects of vegetation (acacia plantations vs. native forests) and soil types (Oxisols vs. Ultisols) on soil properties, including the diversity and community structures of bacteria- and fungi-colonizing surface and subsurface roots and soil in the Central Highlands of Vietnam. The results in surface soil showed that pH was significantly higher in acacia than in native for Oxisols but not for Ultisols, while exchangeable Al was significantly lower in acacia than in native for Ultisols but not for Oxisols. Bacterial alpha diversity (especially within phylum Chloroflexi) was higher in acacia than in native only for Oxisols but not for Ultisols, which was the same statistical result as soil pH but not exchangeable Al. These results suggest that soil pH, but not exchangeable Al, can be the critical factor to determine bacterial diversity. Acacia tree roots supported greater proportions of copiotrophic bacteria, which may support lower contents of soil inorganic N, compared with native tree roots for both Oxisols and Ultisols. Acacia tree roots also supported greater proportions of plant pathogenic Mycoleptodiscus sp. but appeared to reduce the abundances and diversity of beneficial ECM fungi compared with native tree roots regardless of soil types. Such changes in fungal community structures may threaten the sustainable productivity of acacia plantations in the future.
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Affiliation(s)
- Kozue Sawada
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Shinichi Watanabe
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ho Lam Nguyen
- University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Soh Sugihara
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mayuko Seki
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hana Kobayashi
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Koki Toyota
- Institute of Symbiotic Science and Technology, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shinya Funakawa
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
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104
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Microbial Diversity and Ecosystem Functioning in Deadwood of Black Pine of a Temperate Forest. FORESTS 2021. [DOI: 10.3390/f12101418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.
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105
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Beidler KV, Oh YE, Pritchard SG, Phillips RP. Mycorrhizal roots slow the decay of belowground litters in a temperate hardwood forest. Oecologia 2021; 197:743-755. [PMID: 34626268 DOI: 10.1007/s00442-021-05051-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/26/2021] [Indexed: 11/24/2022]
Abstract
There is increasing evidence that plant roots and mycorrhizal fungi, whether living or dead, play a central role in soil carbon (C) cycling. Root-mycorrhizal-microbial interactions can both suppress and enhance litter decay, with the net result dependent upon belowground nutrient acquisition strategies and soil nutrient availability. We measured the net effect of living roots and mycorrhizal fungi on the decay of dead roots and fungal hyphae in a hardwood forest dominated by either sugar maple (Acer saccharum) or white oak (Quercus alba) trees. Root and fungal litter were allowed to decompose within root-ingrowth bags and root-exclusion cores. In conjunction with root effects on decay, we assessed foraging responses and root induced changes in soil moisture, nitrogen (N) availability and enzyme activity. After 1 year, maple root production increased, and mycorrhizal fungal colonization decreased in the presence of decaying litter. In addition, we found that actively foraging roots suppressed the decay of root litter (- 14%) more than fungal litter (- 3%), and suppression of root decay was stronger for oak (- 20%) than maple roots (- 8%). Suppressive effects of oak roots on decay were greatest when roots also reduced soil N availability, which corresponded with reductions in hydrolytic enzyme activity and enhanced oxidative enzyme activities. These findings further our understanding of context-dependent drivers of root-mycorrhizal-microbial interactions and demonstrate that such interactions can play an underappreciated role in soil organic matter accumulation and turnover in temperate forests.
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Affiliation(s)
- Katilyn V Beidler
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - Young E Oh
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Seth G Pritchard
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
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106
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Martinović T, Odriozola I, Mašínová T, Doreen Bahnmann B, Kohout P, Sedlák P, Merunková K, Větrovský T, Tomšovský M, Ovaskainen O, Baldrian P. Temporal turnover of the soil microbiome composition is guild-specific. Ecol Lett 2021; 24:2726-2738. [PMID: 34595822 DOI: 10.1111/ele.13896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023]
Abstract
Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilised repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.
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Affiliation(s)
- Tijana Martinović
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Barbara Doreen Bahnmann
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic.,Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Sedlák
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Kristina Merunková
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Czech Republic
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107
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Ma Y, Feng C, Wang Z, Huang C, Huang X, Wang W, Yang S, Fu S, Chen HY. Restoration in degraded subtropical broadleaved forests induces changes in soil bacterial communities. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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108
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Adamo I, Castaño C, Bonet JA, Colinas C, Martínez de Aragón J, Alday JG. Lack of Phylogenetic Differences in Ectomycorrhizal Fungi among Distinct Mediterranean Pine Forest Habitats. J Fungi (Basel) 2021; 7:jof7100793. [PMID: 34682215 PMCID: PMC8538088 DOI: 10.3390/jof7100793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
Understanding whether the occurrences of ectomycorrhizal species in a given tree host are phylogenetically determined can help in assessing different conservational needs for each fungal species. In this study, we characterized ectomycorrhizal phylogenetic composition and phylogenetic structure in 42 plots with five different Mediterranean pine forests: i.e., pure forests dominated by P. nigra, P. halepensis, and P. sylvestris, and mixed forests of P. nigra-P. halepensis and P. nigra-P. sylvestris, and tested whether the phylogenetic structure of ectomycorrhizal communities differs among these. We found that ectomycorrhizal communities were not different among pine tree hosts neither in phylogenetic composition nor in structure and phylogenetic diversity. Moreover, we detected a weak abiotic filtering effect (4%), with pH being the only significant variable influencing the phylogenetic ectomycorrhizal community, while the phylogenetic structure was slightly influenced by the shared effect of stand structure, soil, and geographic distance. However, the phylogenetic community similarity increased at lower pH values, supporting that fewer, closely related species were found at lower pH values. Also, no phylogenetic signal was detected among exploration types, although short and contact were the most abundant types in these forest ecosystems. Our results demonstrate that pH but not tree host, acts as a strong abiotic filter on ectomycorrhizal phylogenetic communities in Mediterranean pine forests at a local scale. Finally, our study shed light on dominant ectomycorrhizal foraging strategies in drought-prone ecosystems such as Mediterranean forests.
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Affiliation(s)
- Irene Adamo
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Correspondence:
| | - Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden;
| | - José Antonio Bonet
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
| | - Carlos Colinas
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Juan Martínez de Aragón
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Forest Science and Technology Centre of Catalonia, Ctra. Sant Llorenç de Morunys km 2, E25280 Solsona, Spain
| | - Josu G. Alday
- Joint Research Unit CTFC-AGROTECNIO-CERCA, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain; (J.A.B.); (J.M.d.A.); (J.G.A.)
- Department of Crop and Forest Sciences, University of Lleida, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain;
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109
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Bayranvand M, Akbarinia M, Salehi Jouzani G, Gharechahi J, Baldrian P. Distribution of Soil Extracellular Enzymatic, Microbial, and Biological Functions in the C and N-Cycle Pathways Along a Forest Altitudinal Gradient. Front Microbiol 2021; 12:660603. [PMID: 34539590 PMCID: PMC8447401 DOI: 10.3389/fmicb.2021.660603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/23/2021] [Indexed: 11/23/2022] Open
Abstract
The diverse chemical, biological, and microbial properties of litter and organic matter (OM) in forest soil along an altitudinal gradient are potentially important for nutrient cycling. In the present study, we sought to evaluate soil chemical, biological, microbial, and enzymatic characteristics at four altitude levels (0, 500, 1,000, and 1,500 m) in northern Iran to characterize nutrient cycling in forest soils. The results showed that carbon (C) and nitrogen (N) turnover changed with altitude along with microbial properties and enzyme activity. At the lowest altitude with mixed forest and no beech trees, the higher content of N in litter and soil, higher pH and microbial biomass nitrogen (MBN), and the greater activities of aminopeptidases affected soil N cycling. At elevations above 1,000 m, where beech is the dominant tree species, the higher activities of cellobiohydrolase, arylsulfatase, β-xylosidase, β-galactosidase, endoglucanase, endoxylanase, and manganese peroxidase (MnP) coincided with higher basal respiration (BR), substrate-induced respiration (SIR), and microbial biomass carbon (MBC) and thus favored conditions for microbial entropy and C turnover. The low N content and high C/N ratio at 500-m altitude were associated with the lowest microbial and enzyme activities. Our results support the view that the plain forest with mixed trees (without beech) had higher litter quality and soil fertility, while forest dominated by beech trees had the potential to store higher C and can potentially better mitigate global warming.
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Affiliation(s)
- Mohammad Bayranvand
- Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran.,Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Moslem Akbarinia
- Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Centre, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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110
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Cork Oak Forests Soil Bacteria: Potential for Sustainable Agroforest Production. Microorganisms 2021; 9:microorganisms9091973. [PMID: 34576868 PMCID: PMC8472395 DOI: 10.3390/microorganisms9091973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study was to find cork oak PGPR isolates with increased nutrient solubilisation traits, able to promote root morphological changes and/or antagonize cork oak bark phytopathogens. Soils from three cork oak forests with distinct bioclimates (humid, semi-humid and semi-arid) were used for isolating bacteria. From the 7634 colony-forming units, 323 bacterial isolates were biochemically assayed for PGPR traits (siderophores production, phosphate solubilizing and organic acids production), and 51 were found to display all these traits. These PGPR were able to induce root morphological changes on Arabidopsis thaliana, like suppression of primary root growth, increase of lateral roots or root hairs formation. However, the most proficient PGPR displayed specific ability in changing a single root morphological trait. This ability was related not only to bacterial genotype, but also with the environment where bacteria thrived and isolation temperature. Bacteria from semi-arid environments (mainly Bacillus megaterium isolates) could hold a promising tool to enhance plant development. Other isolates (Serratia quinivorens or B. cereus) could be further explored for biocontrol purposes.
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111
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Roy Chowdhury P, Golas SM, Alteio LV, Stevens JTE, Billings AF, Blanchard JL, Melillo JM, DeAngelis KM. The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest. Front Microbiol 2021; 12:666558. [PMID: 34512564 PMCID: PMC8429792 DOI: 10.3389/fmicb.2021.666558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022] Open
Abstract
Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.
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Affiliation(s)
| | - Stefan M. Golas
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Lauren V. Alteio
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Joshua T. E. Stevens
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Andrew F. Billings
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jeffrey L. Blanchard
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Jerry M. Melillo
- The Ecosystems Center, Marine Biological Laboratories, Woods Hole, MA, United States
| | - Kristen M. DeAngelis
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
- Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States
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112
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D'Alò F, Odriozola I, Baldrian P, Zucconi L, Ripa C, Cannone N, Malfasi F, Brancaleoni L, Onofri S. Microbial activity in alpine soils under climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147012. [PMID: 33872894 DOI: 10.1016/j.scitotenv.2021.147012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/05/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
Soil enzymatic activity was assessed in the Stelvio Pass area (Italian Central Alps) aiming to define the possible effects of climate change on microbial functioning. Two sites at two different elevations were chosen, a subalpine (2239 m) and an alpine belt (2604-2624 m), with mean annual air temperature differing by almost 3 °C, coherent with the worst future warming scenario (RCP 8.5) by 2100. The lower altitude site may represent a proxy of the potential future situation at higher altitude after the upward shift of subalpine vegetation due to climate change. Additionally, hexagonal open top chambers (OTCs) were installed at the upper site, to passively increase by about 2 °C the summer inner temperature to simulate short term effects of warming before the vegetation shift takes place. Soil physicochemical properties and the bacterial and fungal abundances of the above samples were also considered. The subalpine soils showed a higher microbial activity, especially for hydrolytic enzymes, higher carbon, ammonium and hydrogen (p < 0.001) contents, and a slightly higher PO4 content (p < 0.05) than alpine soils. Bacterial abundance was higher than fungal abundance, both for alpine and subalpine soils. On the other hand, the short term effect, which increased the mean soil temperature during the peak of the growing season in the OTC, showed to induce scarcely significant differences for edaphic parameters and microbial biomass content among the warmed and control plots. Using the manipulative warming experiments, we demonstrated that warming is able to change the enzyme activity starting from colder and higher altitude sites, known to be more vulnerable to the rising temperatures associated with climate change. Although five-years of experimental warming does not allow us to make bold conclusions, it appeared that warming-induced upwards vegetation shift might induce more substantial changes in enzymatic activities than the short-term effects, in the present vegetation context.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Iñaki Odriozola
- 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.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Via Valleggio 11, 21100 Como, CO, Italy.
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Via Valleggio 11, 21100 Como, CO, Italy.
| | - Lisa Brancaleoni
- Botanical Garden, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy.
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113
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Bali R, Pineault J, Chagnon PL, Hijri M. Fresh Compost Tea Application Does Not Change Rhizosphere Soil Bacterial Community Structure, and Has No Effects on Soybean Growth or Yield. PLANTS (BASEL, SWITZERLAND) 2021; 10:1638. [PMID: 34451683 PMCID: PMC8399032 DOI: 10.3390/plants10081638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023]
Abstract
Soil bacteria drive key ecosystem functions, including nutrient mobilization, soil aggregation and crop bioprotection against pathogens. Bacterial diversity is thus considered a key component of soil health. Conventional agriculture reduces bacterial diversity in many ways. Compost tea has been suggested as a bioinoculant that may restore bacterial community diversity and promote crop performance under conventional agriculture. Here, we conducted a field experiment to test this hypothesis in a soybean-maize rotation. Compost tea application had no influence on bacterial diversity or community structure. Plant growth and yield were also unresponsive to compost tea application. Combined, our results suggest that our compost tea bacteria did not thrive in the soil, and that the positive impacts of compost tea applications reported elsewhere may be caused by different microbial groups (e.g., fungi, protists and nematodes) or by abiotic effects on soil (e.g., contribution of nutrients and dissolved organic matter). Further investigations are needed to elucidate the mechanisms through which compost tea influences crop performance.
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Affiliation(s)
- Rana Bali
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
| | - Jonathan Pineault
- Écomestible Inc., 470 Rue Constable, McMasterVille, QC J3G 1N6, Canada;
| | - Pierre-Luc Chagnon
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
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Liu M, Li X, Zhu R, Chen N, Ding L, Chen C. Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:411-424. [PMID: 33264476 DOI: 10.1111/1758-2229.12913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/19/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.
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Affiliation(s)
- Meiling Liu
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Xinrong Li
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Ruiqing Zhu
- Institute of Biology, Gansu Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Ning Chen
- School of Life Science, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Ling Ding
- Foreign Language School, Linyi University, Linyi, Shandong, 267000, China
| | - Cuiyun Chen
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
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115
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Lindström S, Timonen S, Sundström L. The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae). Microbiologyopen 2021; 10:e1201. [PMID: 34459553 PMCID: PMC8289489 DOI: 10.1002/mbo3.1201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
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Affiliation(s)
- Stafva Lindström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Sari Timonen
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
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116
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Gillespie LM, Hättenschwiler S, Milcu A, Wambsganss J, Shihan A, Fromin N. Tree species mixing affects soil microbial functioning indirectly via root and litter traits and soil parameters in European forests. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | | | - Alexandru Milcu
- CEFEUniv MontpellierCNRSEPHEIRD Montpellier France
- Ecotron Européen de Montpellier Univ MontpellierCNRS Montferrier‐sur‐Lez France
| | - Janna Wambsganss
- Chair of Silviculture Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany
- Geobotany Faculty of Biology University of Freiburg Freiburg Germany
| | - Ammar Shihan
- CEFEUniv MontpellierCNRSEPHEIRD Montpellier France
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117
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Haidar R, Yacoub A, Vallance J, Compant S, Antonielli L, Saad A, Habenstein B, Kauffmann B, Grélard A, Loquet A, Attard E, Guyoneaud R, Rey P. Bacteria associated with wood tissues of Esca-diseased grapevines: functional diversity and synergy with Fomitiporia mediterranea to degrade wood components. Environ Microbiol 2021; 23:6104-6121. [PMID: 34288352 PMCID: PMC9291561 DOI: 10.1111/1462-2920.15676] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/18/2021] [Indexed: 11/30/2022]
Abstract
Fungi are considered to cause grapevine trunk diseases such as esca that result in wood degradation. For instance, the basidiomycete Fomitiporia mediterranea (Fmed) is overabundant in white rot, a key type of wood‐necrosis associated with esca. However, many bacteria colonize the grapevine wood too, including the white rot. In this study, we hypothesized that bacteria colonizing grapevine wood interact, possibly synergistically, with Fmed and enhance the fungal ability to degrade wood. We isolated 237 bacterial strains from esca‐affected grapevine wood. Most of them belonged to the families Xanthomonadaceae and Pseudomonadaceae. Some bacterial strains that degrade grapevine‐wood components such as cellulose and hemicellulose did not inhibit Fmed growth in vitro. We proved that the fungal ability to degrade wood can be strongly influenced by bacteria inhabiting the wood. This was shown with a cellulolytic and xylanolytic strain of the Paenibacillus genus, which displays synergistic interaction with Fmed by enhancing the degradation of wood structures. Genome analysis of this Paenibacillus strain revealed several gene clusters such as those involved in the expression of carbohydrate‐active enzymes, xylose utilization and vitamin metabolism. In addition, certain other genetic characteristics of the strain allow it to thrive as an endophyte in grapevine and influence the wood degradation by Fmed. This suggests that there might exist a synergistic interaction between the fungus Fmed and the bacterial strain mentioned above, enhancing grapevine wood degradation. Further step would be to point out its occurrence in mature grapevines to promote esca disease development.
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Affiliation(s)
- Rana Haidar
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France.,Biology Department, Faculty of Science, Tishreen University, Latakia, Syria
| | - Amira Yacoub
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
| | - Jessica Vallance
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health and Bioresources, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health and Bioresources, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Ahmad Saad
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Birgit Habenstein
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Brice Kauffmann
- IECB, UMS 3033, US001, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, Pessac, 33607, France
| | - Eléonore Attard
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux - UMR 5254, IBEAS Avenue de l'Université, Pau, 64013, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour/E2S UPPA/CNRS, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux - UMR 5254, IBEAS Avenue de l'Université, Pau, 64013, France
| | - Patrice Rey
- INRAE, UMR SAVE, Bordeaux Science Agro, ISVV, University of Bordeaux, Villenave d'Ornon, 33882, France
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118
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Becerra-Lucio AA, Labrín-Sotomayor NY, Becerra-Lucio PA, Trujillo-Elisea FI, Chávez-Bárcenas AT, Machkour-M'Rabet S, Peña-Ramírez YJ. Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery. Curr Microbiol 2021; 78:3417-3429. [PMID: 34244846 DOI: 10.1007/s00284-021-02603-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.
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Affiliation(s)
- Angel A Becerra-Lucio
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Natalia Y Labrín-Sotomayor
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Patricia A Becerra-Lucio
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Flor I Trujillo-Elisea
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México
| | - Ana T Chávez-Bárcenas
- Agrobiologia School, Universidad Michoacana de San Nicolás de Hidalgo, CP 6017, Uruapan, Michoacán, México
| | - Salima Machkour-M'Rabet
- Department of Biodiversity Conservation, El Colegio de la Frontera Sur Unidad Chetumal, Av. Centenario km 5.5, CP 77014, Chetumal, Quintana Roo, México
| | - Yuri J Peña-Ramírez
- Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México.
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119
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Sanaei A, Sayer EJ, Yuan Z, Lin F, Fang S, Ye J, Liu S, Hao Z, Wang X. Soil Stoichiometry Mediates Links Between Tree Functional Diversity and Soil Microbial Diversity in a Temperate Forest. Ecosystems 2021. [DOI: 10.1007/s10021-021-00655-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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120
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Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures. BIOLOGY 2021; 10:biology10070569. [PMID: 34206701 PMCID: PMC8301126 DOI: 10.3390/biology10070569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/26/2022]
Abstract
Simple Summary The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications. Abstract This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
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121
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Vishal V, Munda SS, Singh G, Lal S. Cataloguing the bacterial diversity in the active ectomycorrhizal zone of Astraeus from a dry deciduous forest of Shorea. Biodivers Data J 2021; 9:e63086. [PMID: 34054322 PMCID: PMC8154865 DOI: 10.3897/bdj.9.e63086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/26/2021] [Indexed: 02/01/2023] Open
Abstract
The plant microbiome has been considered one of the most researched areas of microbial biodiversity, yet very little information is available on the microbial communities prevailing in the mushroom's ectomycorrhizosphere. Ectomycorrhizal symbioses often result in the formation of a favourable niche which enables the thriving of various microbial symbionts where these symbionts endorse functions, such as quorum sensing, biofilm formation, volatile microbial compound (VOC) production, regulation of microbial gene expression, symbiosis and virulence. The identification of hidden uncultured microbial communities around the active ectomycorrhizal zone of Astraeus from dry deciduous sal forest of Jharkhand, India was carried out using MinION Oxford Nanopore sequencing of 16S rRNA amplicons genes. High richness of Operational Taxonomic Units (1,905 OTUs) was observed. We recorded 25 distinct phyla. Proteobacteria (36%) was the most abundant phylum, followed by Firmicutes (28%), Actinobacteria (10%) and Bacteroidetes (6%), whereas Gammaproteobacteria was the most abundant class of bacterial communities in the active ectomycorrhizal zone. The ectomycorrhizosphere soil has abundant phosphate-solubilising bacteria (PSB). This is the first report of the ectomycorrhizosphere microbiome associated with Astraeus.
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Affiliation(s)
- Vineet Vishal
- Department of Botany, Dr Shyama Prasad Mukherjee University, Ranchi-834008, India Department of Botany, Dr Shyama Prasad Mukherjee University Ranchi-834008 India.,Department of Botany, Bangabasi Evening College, Kolkata-700009, India Department of Botany, Bangabasi Evening College Kolkata-700009 India
| | - Somnath Singh Munda
- Department of Botany, Dr Shyama Prasad Mukherjee University, Ranchi-834008, India Department of Botany, Dr Shyama Prasad Mukherjee University Ranchi-834008 India
| | - Geetanjali Singh
- Department of Botany, Dr Shyama Prasad Mukherjee University, Ranchi-834008, India Department of Botany, Dr Shyama Prasad Mukherjee University Ranchi-834008 India
| | - Shalini Lal
- Department of Botany, Dr Shyama Prasad Mukherjee University, Ranchi-834008, India Department of Botany, Dr Shyama Prasad Mukherjee University Ranchi-834008 India
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122
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Global Change and Forest Disturbances in the Mediterranean Basin: Breakthroughs, Knowledge Gaps, and Recommendations. FORESTS 2021. [DOI: 10.3390/f12050603] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Forest ecosystems in the Mediterranean Basin are mostly situated in the north of the Basin (mesic). In the most southern and dry areas, the forest can only exist where topography and/or altitude favor a sufficient availability of water to sustain forest biomass. We have conducted a thorough review of recent literature (2000–2021) that clearly indicates large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin, their changes in surface and distribution areas, and the main impacts they have suffered. We have focused on the main trends that emerge from the current literature and have highlighted the main threatens and management solution for the maintenance of these forests. The results clearly indicate large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin. These increasing drought conditions together with over-exploitation, pest expansion, fire and soil degradation, are synergistically driving to forest regression and dieback in several areas of this Mediterranean Basin. These environmental changes have triggered responses in tree morphology, physiology, growth, reproduction, and mortality. We identified at least seven causes of the changes in the last three decades that have led to the current situation and that can provide clues for projecting the future of these forests: (i) The direct effect of increased aridity due to more frequent and prolonged droughts, which has driven Mediterranean forest communities to the limit of their capacity to respond to drought and escape to wetter sites, (ii) the indirect effects of drought, mainly by the spread of pests and fires, (iii) the direct and indirect effects of anthropogenic activity associated with general environmental degradation, including soil degradation and the impacts of fire, species invasion and pollution, (iv) human pressure and intense management of water resources, (v) agricultural land abandonment in the northern Mediterranean Basin without adequate management of new forests, (vi) very high pressure on forested areas of northern Africa coupled with the demographic enhancement, the expansion of crops and higher livestock pressure, and the more intense and overexploitation of water resources uses on the remaining forested areas, and (vii) scarcity and inequality of human management and policies, depending on the national and/or regional governments and agencies, being unable to counteract the previous changes. We identified appropriate measures of management intervention, using the most adequate techniques and processes to counteract these impacts and thus to conserve the health, service capacity, and biodiversity of Mediterranean forests. Future policies should, moreover, promote research to improve our knowledge of the mechanisms of, and the effects on, nutrient and carbon plant-soil status concurrent with the impacts of aridity and leaching due to the effects of current changes. Finally, we acknowledge the difficulty to obtain an accurate quantification of the impacts of increasing aridity rise that warrants an urgent investment in more focused research to further develop future tools in order to counteract the negative effects of climate change on Mediterranean forests.
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123
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Paixão DAA, Tomazetto G, Sodré VR, Gonçalves TA, Uchima CA, Büchli F, Alvarez TM, Persinoti GF, da Silva MJ, Bragatto J, Liberato MV, Franco Cairo JPL, Leme AFP, Squina FM. Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties. Enzyme Microb Technol 2021; 148:109820. [PMID: 34116762 DOI: 10.1016/j.enzmictec.2021.109820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022]
Abstract
Although lignocellulose is the most abundant and renewable natural resource for biofuel production, its use remains under exploration because of its highly recalcitrant structure. Its deconstruction into sugar monomers is mainly driven by carbohydrate-active enzymes (CAZymes). To develop highly efficient and fast strategies to discover biomass-degrading enzymes for biorefinery applications, an enrichment process combined with integrative omics approaches was used to identify new CAZymes. The lignocellulolytic-enriched mangrove microbial community (LignoManG) established on sugarcane bagasse (SB) was enriched with lignocellulolytic bacteria and fungi such as Proteobacteria, Bacteroidetes, Basidiomycota, and Ascomycota. These microbial communities were able to degrade up to 55 % of the total SB, indicating the production of lignocellulolytic enzymes. Metagenomic analysis revealed that the LignoManG harbors 18.042 CAZyme sequences such as of cellulases, hemicellulases, carbohydrate esterases, and lytic polysaccharide monooxygenase. Similarly, our metaproteomic analysis depicted several enzymes from distinct families of different CAZy families. Based on the LignoManG data, a xylanase (coldXynZ) was selected, amplified, cloned, expressed, and biochemically characterized. The enzyme displayed psicrofilic properties, with the highest activity at 15 °C, retaining 77 % of its activity when incubated at 0 °C. Moreover, molecular modeling in silico indicated that coldXynZ is composed of a TIM barrel, which is a typical folding found in the GH10 family, and displayed similar structural features related to cold-adapted enzymes. Collectively, the data generated in this study represent a valuable resource for lignocellulolytic enzymes with potential biotechnological applications.
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Affiliation(s)
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200, Aarhus, Denmark
| | - Victoria Ramos Sodré
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Thiago A Gonçalves
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fernanda Büchli
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Thabata Maria Alvarez
- Graduate Programme in Industrial Biotechnology, Universidade Positivo, Curitiba, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Márcio José da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliano Bragatto
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - João Paulo L Franco Cairo
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.
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Leiva D, Fernández-Mendoza F, Acevedo J, Carú M, Grube M, Orlando J. The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate. MICROBIAL ECOLOGY 2021; 81:965-976. [PMID: 33404820 DOI: 10.1007/s00248-020-01662-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.
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Affiliation(s)
- Diego Leiva
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
- Institute of Biology, University of Graz, Graz, Austria
| | | | - José Acevedo
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Margarita Carú
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Julieta Orlando
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile.
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125
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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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126
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Rocha FI, Ribeiro TG, Fontes MA, Schwab S, Coelho MRR, Lumbreras JF, da Motta PEF, Teixeira WG, Cole J, Borsanelli AC, Dutra IDS, Howe A, de Oliveira AP, Jesus EDC. Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas. Front Microbiol 2021; 12:657508. [PMID: 33967996 PMCID: PMC8097146 DOI: 10.3389/fmicb.2021.657508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/29/2021] [Indexed: 01/04/2023] Open
Abstract
Advancing extensive cattle production is a major threat to biodiversity conservation in Amazonia. The dominant vegetation cover has a drastic impact on soil microbial communities, affecting their composition, structure, and ecological services. Herein, we explored relationships between land-use, soil types, and forest floor compartments on the prokaryotic metacommunity structuring in Western Amazonia. Soil samples were taken in sites under high anthropogenic pressure and distributed along a ±800 km gradient. Additionally, the litter and a root layer, characteristic of the forest environment, were sampled. DNA was extracted, and metacommunity composition and structure were assessed through 16S rRNA gene sequencing. Prokaryotic metacommunities in the bulk soil were strongly affected by pH, base and aluminum saturation, Ca + Mg concentration, the sum of bases, and silt percentage, due to land-use management and natural differences among the soil types. Higher alpha, beta, and gamma diversities were observed in sites with higher soil pH and fertility, such as pasture soils or fertile soils of the state of Acre. When taking litter and root layer communities into account, the beta diversity was significantly higher in the forest floor than in pasture bulk soil for all study regions. Our results show that the forest floor's prokaryotic metacommunity performs a spatial turnover hitherto underestimated to the regional scale of diversity.
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Affiliation(s)
- Fernando Igne Rocha
- Department of Soil, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | | | | | - Stefan Schwab
- National Agrobiology Research Center, Embrapa Agrobiologia, Seropédica, Brazil
| | | | | | | | | | - James Cole
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - Iveraldo dos Santos Dutra
- Department of Support, Production and Animal Health, Universidade Estadual Paulista, Araçatuba, Brazil
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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127
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Modi D, Simard S, Lavkulich L, Hamelin RC, Grayston SJ. Stump removal and tree species composition promote a bacterial microbiome that may be beneficial in the suppression of root disease. FEMS Microbiol Ecol 2021; 97:5923548. [PMID: 33053177 DOI: 10.1093/femsec/fiaa213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/12/2020] [Indexed: 01/04/2023] Open
Abstract
Stumping is an effective forest management practice for reducing the incidence of Armillaria root-rot in regenerating trees, but its impact on the soil bacterial community has not been ascertained. This study investigated the long-term impact of stumping and tree species composition in a 48-year-old trial at Skimikin, British Columbia, on the relative abundance, diversity and taxonomic composition of bacterial communities by sequencing the v4 region of 16S rRNA gene using the Illumina Miseq platform. A total of 108 samples were collected from the forest floor (fermented (F) and humus (H) layers) and mineral soil (A (0-10 cm) and B (10-20 cm) horizons) of 36 plots (half each stumped or unstumped) that were planted with pure stands and admixtures of Douglas-fir, western redcedar and paper birch. Bacterial α-diversity in the B horizon declined with stumping whereas β-diversity was affected both by tree species and stumping treatments, with fir and birch supporting distinct bacterial communities. All horizons of stumped plots of birch and its admixtures were significantly enriched with potential plant growth-promoting bacteria. In conclusion, stumping along with planting birch alone or in admixture with other species promotes a bacterial microbiome that appears beneficial in the suppression of root disease.
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Affiliation(s)
- Dixi Modi
- Department of Soil Science, Land and Food Systems, University of British Columbia, 248-2357 Main Mall, Vancouver, BC V6T 1Z4BC V6T 1Z4s Canada
| | - Suzanne Simard
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Les Lavkulich
- Department of Soil Science, Land and Food Systems, University of British Columbia, 248-2357 Main Mall, Vancouver, BC V6T 1Z4BC V6T 1Z4 Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Sue J Grayston
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
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128
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Bayranvand M, Akbarinia M, Salehi Jouzani G, Gharechahi J, Kooch Y, Baldrian P. Composition of soil bacterial and fungal communities in relation to vegetation composition and soil characteristics along an altitudinal gradient. FEMS Microbiol Ecol 2021; 97:5918382. [PMID: 33021633 DOI: 10.1093/femsec/fiaa201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/01/2020] [Indexed: 11/12/2022] Open
Abstract
The objective of the present study was to evaluate how altitudinal gradients shape the composition of soil bacterial and fungal communities, humus forms and soil properties across six altitude levels in Hyrcanian forests. Soil microbiomes were characterized by sequencing amplicons of selected molecular markers. Soil chemistry and plant mycorrhizal type were the two dominant factors explaining variations in bacterial and fungal diversity, respectively. The lowest altitude level had more favorable conditions for the formation of mull humus and exhibited higher N and Ca contents. These conditions were also associated with a higher proportion of Betaproteobacteria, Acidimicrobia, Acidobacteria and Nitrospirae. Low soil and forest floor quality as well as lower bacterial and fungal diversity characterized higher altitude levels, along with a high proportion of shared bacterial (Thermoleophilia, Actinobacteria and Bacilli) and fungal (Eurotiomycetes and Mortierellomycota) taxa. Beech-dominated sites showed moderate soil quality and high bacterial (Alphaproteobacteria, Acidobacteria, Planctomycetes and Bacteroidetes) and fungal (Basidiomycota) diversity. Particularly, the Basidiomycota were well represented in pure beech forests at an altitude of 1500 m. In fertile and nitrogen rich soils with neutral pH, soil quality decreased along the altitudinal gradient, indicating that microbial diversity and forest floor decomposition were likely constrained by climatic conditions.
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Affiliation(s)
- Mohammad Bayranvand
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Moslem Akbarinia
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd., P.O. Box:31535-1897, Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Centre, Baqiyatallah University of Medical Sciences, Vanak Square, Shahid Nosrati Alley, P.O. Box: 1435916471, Tehran, Iran
| | - Yahya Kooch
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4 14220, Czech Republic
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129
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Bowd EJ, Banks SC, Bissett A, May TW, Lindenmayer DB. Direct and indirect disturbance impacts in forests. Ecol Lett 2021; 24:1225-1236. [PMID: 33830614 DOI: 10.1111/ele.13741] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 01/16/2023]
Abstract
Human and natural disturbances are key drivers of change in forest ecosystems. Yet, the direct and indirect mechanisms which underpin these changes remain poorly understood at the ecosystem level. Here, using structural equation modelling across a 150+ year chronosequence, we disentangle the direct and indirect effects of major disturbances in a temperate forest ecosystem. We show that wildfires, logging and post-fire (salvage) logging can affect plant and microbial communities and abiotic soil properties both directly and indirectly through plant-soil-microbial interactions. We quantified 68 direct and indirect disturbance effects across these components, with the majority resulting in ecosystem-wide adverse effects. Indirect disturbance effects accounted for 43% of total disturbance effects, with some amplifying or partially mitigating direct disturbance effects. Overall, human disturbances were associated with more negative effects than natural disturbances. Our analyses provide novel insights into the multifaceted dynamics of forest disturbances and the mechanisms which underpin their relative impacts.
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Affiliation(s)
- Elle J Bowd
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, 2601, Australia.,Research Institute for Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT, 0909, Australia
| | - Andrew Bissett
- The Commonwealth Scientific and Industrial Research Organization, CSIRO Oceans and Atmosphere, Hobart, TAS, 700, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Vic., 3004, Australia
| | - David B Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, 2601, Australia
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130
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Guo Z, Zhang X, Dungait JAJ, Green SM, Wen X, Quine TA. Contribution of soil microbial necromass to SOC stocks during vegetation recovery in a subtropical karst ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143945. [PMID: 33360125 DOI: 10.1016/j.scitotenv.2020.143945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Carbon sequestration is a key soil function, and an increase in soil organic carbon (SOC) is an indicator of ecosystem recovery because it underpins other ecosystem services by acting as a substrate for the soil microbial community. The soil microbial community constitutes the active pool of SOC, and its necromass (microbial residue carbon, MRC) contributes strongly to the stable SOC pool. Therefore, we propose that the potential for restoration of degraded karst ecosystems lies in the abundance of soil microbial community and the persistence of its necromass, and may be measured by changes in its contribution to the active and stable SOC pools during recovery. We investigated changes in SOC stocks using an established space-for-time chronosequence along a perturbation gradient in the subtropical karst ecosystem: sloping cropland < abandoned cropland < shrubland < secondary forest < primary forest. Microbial biomarkers were extracted from soil profiles from surface to bedrock and used to measure the contributions of the soil microbial community composition (using phospholipid fatty acids, PLFAs) and MRC (using amino sugars) to SOC stocks at each recovery stage. The results showed that the SOC stocks ranged from 10.53 to 31.77 kg m-2 and increased with recovery stage, with total MRC accounting for 17-28% of SOC. Increasing PLFAs and MRC abundances were positively correlated with improved soil structure (decreased bulk density) and organic carbon, nitrogen and phosphorus nutrient. Bacterial MRC contributes more to SOC stocks than fungal residue carbon during vegetation recovery. The PLFA analysis indicated that Gram positive bacteria were the largest microbial group and were relatively more abundant in deeper soils, and biomarkers for saprophytic and ectomycorrhizal fungi were more abundant in soils under woody vegetation. In conclusion, this study suggests that the soil microbial community in karst soils have the potential to adapt to changing soil conditions and contribute substantially to building SOC stocks after abandonment of agriculture in degraded karst landscapes.
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Affiliation(s)
- Zhiming Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyu Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jennifer A J Dungait
- Geography, College of Life and Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK; Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK
| | - Sophie M Green
- Geography, College of Life and Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK
| | - Xuefa Wen
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Timothy A Quine
- Geography, College of Life and Environmental Sciences, University of Exeter, Rennes Drive, Exeter EX4 4RJ, UK
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131
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Dom SP, Ikenaga M, Lau SYL, Radu S, Midot F, Yap ML, Chin MY, Lo ML, Jee MS, Maie N, Melling L. Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia. Sci Rep 2021; 11:6416. [PMID: 33742002 PMCID: PMC7979770 DOI: 10.1038/s41598-021-81865-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.
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Affiliation(s)
- Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei-Yee Chin
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nagamitsu Maie
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Lulie Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
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132
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Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 2021; 97:fiab022. [PMID: 33547899 PMCID: PMC7948073 DOI: 10.1093/femsec/fiab022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - O Janne Kjønaas
- NIBIO, Department of Terrestrial Ecology, NO-1431 Ås, Norway
| | - Luis N Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Yngvild Ransedokken
- Faculty of Environmental and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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133
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Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers. J Fungi (Basel) 2021; 7:jof7030185. [PMID: 33807546 PMCID: PMC7998857 DOI: 10.3390/jof7030185] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO2) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO2 emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO2 assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO2 emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.
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134
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Teng J, Tian J, Yu G, Kuzyakov Y. Soil properties and root traits jointly shape fine-scale spatial patterns of bacterial community and metabolic functions within a Korean pine forest. PeerJ 2021; 9:e10902. [PMID: 33680578 PMCID: PMC7919533 DOI: 10.7717/peerj.10902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Spatial heterogeneity of soil bacterial community depends on scales. The fine-scale spatial heterogeneity of bacterial community composition and functions remains unknown. We analyzed the main driving factors of fine-scale spatial patterns of soil bacterial community composition and carbon metabolic functions across a 30 m × 40 m plot within a Korean pine forest by combining Illumina 16S rRNA sequencing with Biolog Ecoplates based on 53 soil samples. Clear spatial patterns in bacterial community composition and metabolic functions were observed in the forest soil. The bacterial community composition and metabolic functions both showed distance-decay of similarity within a distance of meters. Structural equation model analysis revealed that environmental variables and geographic distance together explained 37.9% and 63.1% of community and metabolic functions, respectively. Among all environmental factors, soil organic carbon (SOC) and root biomass emerged as the most important drivers of the bacterial community structure. In contrast, soil pH explained the largest variance in metabolic functions. Root biomass explained the second-largest variance in soil bacterial community composition, but root traits made no difference in metabolic functions variance. These results allow us to better understand the mechanisms controlling belowground diversity and plant-microbe interactions in forest ecosystems.
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Affiliation(s)
- Jialing Teng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Tian
- College of Resources and Environmental Sciences; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany.,Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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135
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Fracchia F, Mangeot-Peter L, Jacquot L, Martin F, Veneault-Fourrey C, Deveau A. Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities. Appl Environ Microbiol 2021; 87:e02541-20. [PMID: 33452025 PMCID: PMC8105020 DOI: 10.1128/aem.02541-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/21/2020] [Indexed: 11/24/2022] Open
Abstract
Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host.IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.
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Affiliation(s)
- F Fracchia
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | | - L Jacquot
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - F Martin
- Université de Lorraine, INRAE, IAM, Nancy, France
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Haidian District, Beijing, China
| | | | - A Deveau
- Université de Lorraine, INRAE, IAM, Nancy, France
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136
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Ogola HJO, Selvarajan R, Tekere M. Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome. Front Microbiol 2021; 12:592725. [PMID: 33716998 PMCID: PMC7943610 DOI: 10.3389/fmicb.2021.592725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30-55°; open canopy cover, <30%), mid (less steep, 15-30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20-65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent β-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.
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Affiliation(s)
- Henry Joseph Oduor Ogola
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Ramganesh Selvarajan
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
| | - Memory Tekere
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, South Africa
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137
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Zhu Q, Wang N, Duan B, Wang Q, Wang Y. Rhizosphere bacterial and fungal communities succession patterns related to growth of poplar fine roots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:143839. [PMID: 33298322 DOI: 10.1016/j.scitotenv.2020.143839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/12/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Understanding the succession patterns of microbial community along root growth provides deep insights into interaction between fine roots and microbes. In the study, we investigated this issue using fine roots from poplar trees and grouped these fine roots into three growth stages: newborn white roots (WR), mature yellow roots (YR) and aging brown roots (BR). Root surface traits were observed under a scanning electron microscopy (SEM). Adhered soils on roots of the three growth stages were grouped into the three soil compartments, correspondingly. The 16S rRNA and ITS1 region were sequenced for bacteria and fungi inhabiting rhizosphere soils, respectively. Phospholipid fatty acid (PLFA) technology was employed to examine the biomass of bacterial and fungal communities. The anatomical traits of fine roots show apparent differences among the WR, YR and BR. Both bacteria and fungi have 25 dominant genera with a relative abundance over 1%, of which, four genera of the bacteria (Bacillus, Burkholderia, Ralstonia and Dyella) differ in abundance among the WR, YR and BR soil compartments and four genera of the fungi (Fusarium, Chaetomium, Penicillium and Scleroderma) differ in abundance among these soil compartments. The operational taxonomic units (OTUs) showed the highest richness in the WR soil compartment for bacteria and in the YR soil compartment for fungi, indicating a different succession pattern between the bacterial and fungal communities. Furthermore, the biomass of bacterial community is larger than the fungal community according to PLFAs, and both decreased along fine root growth. The total carbon (TC) in the soil increases along root growth while the dissolved organic carbon (DOC) decreases. Redundancy analysis (RDA) shows a close correlation between twelve dominant bacteria genera and the total organic carbon (TOC), the readily oxidizable organic carbon (ROC) and DOC and ten dominant fungi genera with the TOC and ROC. In conclusion, our results indicate that fine roots growth has shaped the composition and structure of root associated bacterial and fungal communities.
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Affiliation(s)
- Qiliang Zhu
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China
| | - Nian Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China
| | - Baoli Duan
- Institute of Mountain Hazards and Environments, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Qingkui Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, PR China
| | - Yanping Wang
- Taishan Forest Ecosystem Research Station of State Forestry Administration, College of Forestry, Shandong Agricultural University, Tai'an 271018, PR China.
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138
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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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139
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Stewart JD, Ontai A, Yusoof K, Ramirez KS, Bilinski T. Functional redundancy in local spatial scale microbial communities suggests stochastic processes at an urban wilderness preserve in Austin, TX, USA. FEMS Microbiol Lett 2021; 368:6122587. [PMID: 33507263 DOI: 10.1093/femsle/fnab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022] Open
Abstract
Empirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales; however, less is known at smaller spatial scales. The goal of this research was to evaluate relationships between ecosystem characteristics and bacterial community structure/function at broad taxonomic resolutions in soils across small spatial scales. We employed 16S rRNA gene sequencing, community-level physiological profiling and soil chemical analysis to address this goal. We found weak relationships between gradients in soil characteristics and community structure/function. Specific operational taxonomic units did not respond to edaphic variation, but Acidobacteria, Bacteroidetes and Nitrospirae shifted their relative abundances. High metabolic diversity within the bacterial communities was observed despite general preference of Tween 40/80. Carbon metabolism patterns suggest dominance of functional specialists at our times of measurement. Pairwise comparison of carbon metabolism patterns indicates high levels of functional redundancy. Lastly, at broad taxonomic scales, community structure and function weakly covary with edaphic properties. This evidence suggests that stochasticity or unmeasured environmental gradients may be influential in bacterial community assembly in soils at small spatial scales.
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Affiliation(s)
- Justin D Stewart
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
| | - Amy Ontai
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, 06520, New Haven, CT, USA
| | - Kizil Yusoof
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center, 78249, San Antonio, TX, USA
| | - Kelly S Ramirez
- Department of Biological Sciences, The University of Texas at El Paso, 79968, El Paso, TX, USA
| | - Teresa Bilinski
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309, Boulder, CO, USA
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140
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Abstract
Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood’s properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
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141
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Moya D, Fonturbel MT, Lucas-Borja ME, Peña E, Alfaro-Sanchez R, Plaza-Álvarez PA, González-Romero J, de Las Heras J. Burning season and vegetation coverage influenced the community-level physiological profile of Mediterranean mixed-mesogean pine forest soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 277:111405. [PMID: 33032003 DOI: 10.1016/j.jenvman.2020.111405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 09/08/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of forest soil ecology is necessary to assess vulnerability to disturbances, such as wildfires, and improve its microbial diversity and functional value. Soil microbiota play an important role in forest soil processes and are a key driver of postfire recovery, but they are very vulnerable to heat. According to future scenarios for climate and land-use change, fire regimes will undergo transformations in semiarid terrestrial ecosystems, mainly in the Mediterranean Basin. To develop tools for forest management in fire-prone areas, i.e., fire prevention, we assessed the impact of prescribed burnings on soil microorganisms in Mediterranean mixed pine forests. We hypothesised that low severity fire burns would not influence the functional diversity of soil microorganisms, although the burning season could influence that response due to seasonal variations in its vulnerability. We used the Biolog EcoPlate System to record soil biological indicators and assess the effect of the prescribed burning season (early or late season) on bacterial communities, including the soil-plant interphase. The soil microbiome response differed significantly according to vegetation coverage but prescribed burning season was not directly related. Burning increased the proportions of soil organic matter and soil organic carbon, and also promoted cation-exchange capacity and total phosphorus, which were higher following spring burns. Microbial richness and the Shannon-Weaver diversity index both showed a positive correlation with vegetation cover. However, microbial richness was triggered after burning uncovered patches of vegetation. We also noted differences in the usage pattern for the six substrate groups defined in our study: the use of carboxylic acids, amino acids and carbohydrates was higher in unburned plots and those subject to late burns, whereas amino acids did not predominate in early burn plots.
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Affiliation(s)
- D Moya
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain.
| | - M T Fonturbel
- Centro de Investigación Forestal-Lourizán, Consellería do Medio Rural, Xunta de Galicia, P.O. Box 127, 36080, Pontevedra, Spain
| | - M E Lucas-Borja
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - E Peña
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - R Alfaro-Sanchez
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - P A Plaza-Álvarez
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - J González-Romero
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
| | - J de Las Heras
- Forest Ecology Research Group (ECOFOR), Escuela Técnica Superior Ingenieros Agrónomos y Montes, Universidad de Castilla-La Mancha, Campus Universitario, 02071, Albacete, Spain
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142
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Praeg N, Illmer P. Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms. Sci Rep 2020; 10:22324. [PMID: 33339837 PMCID: PMC7749151 DOI: 10.1038/s41598-020-79143-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 12/01/2020] [Indexed: 02/05/2023] Open
Abstract
Microbial community and diversity in the rhizosphere is strongly influenced by biotic and/or abiotic factors, like root exudates, nutrient availability, edaphon and climate. Here we report on the microbial diversity within the rhizosphere of Larix decidua, a dominant tree species in the Alps, as compared with the microbiome within the surrounding soil. We describe how increased light intensity influenced the rhizobiome and put emphasize on methane cycling microorganisms. Microbial taxa were classified into 26 bacterial, 4 archaeal and 6 fungal phyla revealing significant differences between bulk and rhizosphere soils. The dominant prokaryotic phyla were Proteobacteria, Acidobacteria, Actinobacteria (both, rhizosphere and bulk soil) and Bacteroidetes (rhizosphere soil only) and dominant fungal phyla in both fractions included Ascomycota and Basidiomycota. The rhizosphere community was indicated by Suillus sp., plant growth-promoting bacteria and Candidatus Saccharibacteria. Predicted genes in membrane transport and carbohydrate metabolism were significantly more abundant in rhizosphere soils while genes connected with energy metabolisms and cell motility increased in bulk soils. Dominant methanotrophic microorganisms were Upland Soil Cluster (USC) α methanotrophs, Methylogaea spp. and Methylosinus spp., while most methanogens belonged to Methanomassiliicoccales. The overall abundance of methanotrophs distinctly increased in the rhizosphere but to a very different species-specific extent. The increased light intensity only led to minor changes in the rhizobiome, nevertheless a couple of indicator species (e.g. Pseudomonas sp.) for intensified light conditions were established.
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Affiliation(s)
- Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25d, 6020, Innsbruck, Austria.
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25d, 6020, Innsbruck, Austria
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143
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Mushinski RM, Payne ZC, Raff JD, Craig ME, Pusede SE, Rusch DB, White JR, Phillips RP. Nitrogen cycling microbiomes are structured by plant mycorrhizal associations with consequences for nitrogen oxide fluxes in forests. GLOBAL CHANGE BIOLOGY 2020; 27:1068-1082. [PMID: 33319480 PMCID: PMC7898693 DOI: 10.1111/gcb.15439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Volatile nitrogen oxides (N2 O, NO, NO2 , HONO, …) can negatively impact climate, air quality, and human health. Using soils collected from temperate forests across the eastern United States, we show microbial communities involved in nitrogen (N) cycling are structured, in large part, by the composition of overstory trees, leading to predictable N-cycling syndromes, with consequences for emissions of volatile nitrogen oxides to air. Trees associating with arbuscular mycorrhizal (AM) fungi promote soil microbial communities with higher N-cycle potential and activity, relative to microbial communities in soils dominated by trees associating with ectomycorrhizal (ECM) fungi. Metagenomic analysis and gene expression studies reveal a 5 and 3.5 times greater estimated N-cycle gene and transcript copy numbers, respectively, in AM relative to ECM soil. Furthermore, we observe a 60% linear decrease in volatile reactive nitrogen gas flux (NOy ≡ NO, NO2 , HONO) as ECM tree abundance increases. Compared to oxic conditions, gas flux potential of N2 O and NO increase significantly under anoxic conditions for AM soil (30- and 120-fold increase), but not ECM soil-likely owing to small concentrations of available substrate ( NO 3 - ) in ECM soil. Linear mixed effects modeling shows that ECM tree abundance, microbial process rates, and geographic location are primarily responsible for variation in peak potential NOy flux. Given that nearly all tree species associate with either AM or ECM fungi, our results indicate that the consequences of tree species shifts associated with global change may have predictable consequences for soil N cycling.
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Affiliation(s)
- Ryan M. Mushinski
- School of Life SciencesUniversity of WarwickCoventryUK
- O'Neill School of Public and Environmental AffairsIndiana UniversityBloomingtonINUSA
| | - Zachary C. Payne
- O'Neill School of Public and Environmental AffairsIndiana UniversityBloomingtonINUSA
- Department of ChemistryIndiana UniversityBloomingtonINUSA
| | - Jonathan D. Raff
- O'Neill School of Public and Environmental AffairsIndiana UniversityBloomingtonINUSA
- Department of ChemistryIndiana UniversityBloomingtonINUSA
| | - Matthew E. Craig
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Sally E. Pusede
- Department of Environmental SciencesUniversity of VirginiaCharlottesvilleVAUSA
| | - Douglas B. Rusch
- Center for Genomics and BioinformaticsIndiana UniversityBloomingtonINUSA
| | - Jeffrey R. White
- O'Neill School of Public and Environmental AffairsIndiana UniversityBloomingtonINUSA
- Department of Earth and Atmospheric SciencesIndiana UniversityBloomingtonINUSA
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Byers AK, Condron L, Donavan T, O'Callaghan M, Patuawa T, Waipara N, Black A. Soil microbial diversity in adjacent forest systems - contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest. FEMS Microbiol Ecol 2020; 96:5808812. [PMID: 32179899 PMCID: PMC7161737 DOI: 10.1093/femsec/fiaa047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/15/2020] [Indexed: 12/26/2022] Open
Abstract
Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.
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Affiliation(s)
- Alexa-Kate Byers
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
| | - Leo Condron
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
| | - Tom Donavan
- Te Roroa Group, P.O. Box 6, Waimamaku 0446, New Zealand
| | | | - Taoho Patuawa
- Te Roroa Group, P.O. Box 6, Waimamaku 0446, New Zealand
| | - Nick Waipara
- Institute of Plant and Food Research, Sandringham, Auckland 1025, New Zealand
| | - Amanda Black
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
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145
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Gonzalo M, Deveau A, Aigle B. Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil. MICROBIAL ECOLOGY 2020; 80:872-884. [PMID: 32879989 DOI: 10.1007/s00248-020-01579-6] [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: 07/30/2019] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.
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Affiliation(s)
- Milena Gonzalo
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France
| | - Aurélie Deveau
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France.
| | - Bertrand Aigle
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France.
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146
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Islam W, Noman A, Naveed H, Huang Z, Chen HYH. Role of environmental factors in shaping the soil microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:41225-41247. [PMID: 32829437 DOI: 10.1007/s11356-020-10471-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/10/2020] [Indexed: 05/09/2023]
Abstract
The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.
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Affiliation(s)
- Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, 38000, Pakistan
| | - Hassan Naveed
- College of Life Science, Leshan Normal University, Leshan, 614004, Sichuan, China
| | - Zhiqun Huang
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
| | - Han Y H Chen
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
- Institute of Geography, Fujian Normal University, Fuzhou, 350007, China.
- Faculty of Natural Resources Management, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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147
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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148
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Influence of Acacia mangium on Soil Fertility and Bacterial Community in Eucalyptus Plantations in the Congolese Coastal Plains. SUSTAINABILITY 2020. [DOI: 10.3390/su12218763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Productivity and sustainability of tropical forest plantations greatly rely on regulation of ecosystem functioning and nutrient cycling, i.e., the link between plant growth, nutrient availability, and the microbial community structure. So far, these interactions have never been evaluated in the Acacia and Eucalyptus forest planted on infertile soils in the Congolese coastal plains. In the present work, the soil bacterial community has been investigated by metabarcoding of the 16S rRNA bacterial gene in different stands of monoculture and mixed-species plantation to evaluate the potential of nitrogen-fixing trees on nutrient and bacterial structure. At the phylum level, the soil bacterial community was dominated by Actinobacteria, followed by Proteobacteria, Firmicutes, and Acidobacteria. A principal coordinate analysis revealed that bacterial communities from pure Eucalyptus, compared to those from plantations containing Acacia in pure and mixed-species stands, showed different community composition (beta-diversity). Regardless of the large variability of the studied soils, the prevalence of Firmicutes phylum, and lower bacterial richness and phylogenic diversity were reported in stands containing Acacia relative to the pure Eucalyptus. Distance-based redundancy analysis revealed a positive correlation of available phosphorus (P) and carbon/nitrogen (C/N) ratio with bacterial community structure. However, the Spearman correlation test revealed a broad correlation between the relative abundance of bacterial taxa and soil attributes, in particular with sulfur (S) and carbon (C), suggesting the important role of soil bacterial community in nutrient cycling in this type of forest management. Concerning mixed plantations, a shift in bacterial community structure was observed, probably linked to other changes, i.e., improvement in soil fertility (enhanced P and C dynamics in forest floor and soil, and increase in soil N status), and C sequestration in both soil and stand wood biomass with the great potential impact to mitigate climate change. Overall, our findings highlight the role of soil attributes, especially C, S, available P, and C/N ratio at a lesser extent, in driving the soil bacterial community in mixed-species plantations and its potential to improve soil fertility and to sustain Eucalyptus plantations established on the infertile and sandy soils of the Congolese coastal plains.
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149
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Prada-Salcedo LD, Wambsganss J, Bauhus J, Buscot F, Goldmann K. Low root functional dispersion enhances functionality of plant growth by influencing bacterial activities in European forest soils. Environ Microbiol 2020; 23:1889-1906. [PMID: 32959469 DOI: 10.1111/1462-2920.15244] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Current studies show that multispecies forests are beneficial regarding biodiversity and ecosystem functionality. However, there are only little efforts to understand the ecological mechanisms behind these advantages of multispecies forests. Bacteria are among the key plant growth-promoting microorganisms that support tree growth and fitness. Thus, we investigated links between bacterial communities, their functionality and root trait dispersion within four major European forest types comprising multispecies and monospecific plots. Bacterial diversity revealed no major changes across the root functional dispersion gradient. In contrast, predicted gene profiles linked to plant growth activities suggest an increasing bacterial functionality from monospecific to multispecies forest. In multispecies forest plots, the bacterial functionality linked to plant growth activities declined with the increasing functional dispersion of the roots. Our findings indicate that enriched abundant bacterial operational taxonomic units are decoupled from bacterial functionality. We also found direct effects of tree species identity on bacterial community composition but no significant relations with root functional dispersion. Additionally, bacterial network analyses indicated that multispecies forests have a higher complexity in their bacterial communities, which points towards more stable forest systems with greater functionality. We identified a potential of root dispersion to facilitate bacterial interactions and consequently, plant growth activities.
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Affiliation(s)
- Luis Daniel Prada-Salcedo
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,Department of Biology, University of Leipzig, Leipzig, Johannisallee 21, 04103, Germany
| | - Janna Wambsganss
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany.,Chair of Geobotany, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestraße 1, 79104, Germany
| | - Jürgen Bauhus
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Tennenbacherstr. 4, 79085, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Deutscher Platz 5e, 04103, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Theodor-Lieser-Straße 4, 06120, Germany
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150
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Jefanova O, Baužienė I, Lujanienė G, Švedienė J, Raudonienė V, Bridžiuvienė D, Paškevičius A, Levinskaitė L, Žvirgždas J, Petrošius R, Skuratovič Ž, Mažeika J. Initiation of radioecological monitoring of forest soils and plants at the Lithuanian border region before the start of the Belarusian nuclear power plant operation. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:666. [PMID: 33001295 DOI: 10.1007/s10661-020-08638-y] [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: 04/14/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Knowledge of the background activity concentrations of anthropogenic radionuclides before the start of operation of the new nuclear power plant in Belarus, BelNPP, is an issue of great importance for neighbouring countries. In this study, we provide the pilot characterisation of the Lithuanian part of the 30-km zone of the BelNPP, emphasising the forest plants, terrestrial mosses, forest organic and mineral topsoil to describe the preoperational radioecological state of the pine forest ecosystem. Key anthropogenic radionuclides (14C, 3H, 137Cs and 239,240Pu) were analysed. The 14C specific activity varied from 97.80 ± 1.30 to 102.40 ± 0.79 pMC. The 3H specific activity in the tissue-free water tritium form varied from 13.2 ± 2.2 TU to 20.8 ± 2.3 TU, which corresponded to the 3H level of precipitation in this region. The activity concentrations of 239,240Pu in soil and moss samples did not exceed 1 Bq/kg and were mainly due to global fallout after nuclear tests. The 137Cs inventory in the pine forest soils of the Lithuanian part of the BelNPP 30-km zone varied from 930 ± 70 to 1650 ± 430 Bq/m2. High variation of the inventory and uneven distribution in the soil profile conditioned a wide range of 137Сs activity in terrestrial plants from 1.0 ± 0.5 to 40.5 ± 1.8 Bq/kg dry weight. The abundance of microorganisms in different seasons and soil depths do not exceed the natural levels. According to PCA loads, the number of microorganisms and variability of 137Cs specific activity is determined by soil abiotic parameters.
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Affiliation(s)
- Olga Jefanova
- Laboratory of Nuclear Geophysics and Radioecology, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Ieva Baužienė
- Laboratory of Geoenvironmental Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania.
| | - Galina Lujanienė
- Department of Environmental Research, State Research Institute Center for Physical Sciences and Technology, Saulėtekio av. 3, 10257, Vilnius, Lithuania
| | - Jurgita Švedienė
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Vita Raudonienė
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Danguolė Bridžiuvienė
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Algimantas Paškevičius
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Loreta Levinskaitė
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Jonas Žvirgždas
- Laboratory of Biodeterioration Research, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Rimantas Petrošius
- Laboratory of Nuclear Geophysics and Radioecology, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Žana Skuratovič
- Laboratory of Nuclear Geophysics and Radioecology, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Jonas Mažeika
- Laboratory of Nuclear Geophysics and Radioecology, State Institute Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
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