Drivers of microbial community structure in forest soils

Lladó, Salvador; López-Mondéjar, Rubén; Baldrián, Petr

doi:10.1007/s00253-018-8950-4

Cited by 183 publications

(138 citation statements)

References 85 publications

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“…Therefore, an enrichment on taxa that are known to include many copiotrophic members (as Proteobacteria; Trivedi et al, 2013) could be related with the presence of many residual roots, as was the case of our sampled soil cores. This is in agreement with other reports describing differences in the bacterial composition of bulk or rhizospheric soils (Lladó et al, 2018). Within Proteobacteria, Alphaproteobacteria was the most conspicuous identified class in cork oak soils, representing 21% of total reads (65% of Proteobacteria reads, Fig.…”

Section: Resultssupporting

confidence: 92%

Climatic impacts on the bacterial community profiles of cork oak soils

Reis

Soares-Castro

Costa

et al. 2019

Applied Soil Ecology

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Climate changes comprise increasing global temperature and water cycle deregulation (precipitation storms and long dry seasons). Many affected ecosystems are located within the Mediterranean basin, where cork oak (Quercus suber L.) is one of the most important forest ecosystems. Despite cork oak tolerance to drought, the decrease of water availability and increase of temperature is causing a serious decline of cork oak populations. In the present work, the bacterial community of cork oak soils was assessed by metabarcoding using Illumina Miseq. Soils from seven independent cork oak forests were collected along a climate gradient. In all forest soils, Proteobacteria and Actinobacteria were the richest and more abundant bacteria. Acidobacteria also presented a high relative abundance, and Chloroflexi was a rich phylum. The soil bacterial community diversity and composition was strongly affected by the climatic region where cork oak resides and specific bacterial taxa were differently affected by precipitation and temperature. Accordingly, cork oak bacterial communities clustered into three distinct groups, related with humid, sub-humid and arid/semi-arid climates. Driest and warmer forests presented more diverse bacterial communities than humid and coolest forests. However, driest climates presented more homogenous bacterial communities among forests than humid climates. Climate (mainly precipitation) revealed to be the strongest driver leading to significant variations of bacterial community profiles. The most impacted bacterial taxa by climatic variables were Proteobacteria, in particular Gammaproteobacteria and Deltaproteobacteria, Chloroflexi, and Firmicutes. Humid forests presented mainly Acidobacteria as good indicators of climate, whereas Actinobacteria members were better indicators for arid forests (mainly Gaiellales and Frankiales). Some indicator species for different climate conditions were members of the bacterial core of cork oak stands (7% of the total bacterial community). Taken together, different microbiomes were selected by the climate conditions in cork oak stands along a climate gradient and might provide the key to forest sustainability in times of global warming. challenge to cork oak forests (reviewed by Reis et al., 2017; Maghnia et al., 2019). An adaptation of cork oak populations to drier and warmer conditions is expectable (Varela et al., 2015), but the decline of existing populations have been described all over Mediterranean basin (reviewed by Reis et al., 2017). From the huge diversity of microbes present in cork oak soils, fungal communities are those more related with water transfer and increasing water availability to plants. This is mostly due to the ability of ectomycorrhizal fungi to become associated to cork oak roots, promoting water and nutrients transfer (Reis et al., 2017). However, bacteria also play an important ecological role on forest soils. Besides being important for decomposition of organic matter, N fixation, mineral weathering and consequently the release of inorg...

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Section: Resultssupporting

confidence: 92%

Climatic impacts on the bacterial community profiles of cork oak soils

Reis

Soares-Castro

Costa

et al. 2019

Applied Soil Ecology

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“…This larger role of microenvironment versus stochastic factors has repeatedly been seen in soil communities, where soils with similar environmental characteristics have similar microbial communities regardless of geographic distance (Fierer and Jackson, 2006;Lauber et al, 2009;Xu et al, 2014;Lladó et al, 2018;Plassart et al, 2019). Interestingly, we see this same trend in the bacterial communities of the soil-dwelling salamanders sampled in this study.…”

Section: Community Diversity and Compositionsupporting

confidence: 83%

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Barnes

Carter

2020

Front. Microbiol.

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Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.

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“…In different development stage, the utilization of nutrient substance would determine the recruitment of required fungi, and microbial growth rates must be seen in light of the root growth rates (Kuzyakov & Razavi, ). The components of root exudates are connected with stand age, with different root exudates directly influencing the proportion and community structure of rhizosphere microorganisms (Broeckling, Broz, Bergelson, Manter, & Vivanco, ; Llado, Lopez‐Mondejar, & Baldrian, ).…”

Section: Discussionmentioning

confidence: 99%

Community structure and functional group of root‐associated Fungi of Pinus sylvestris var. mongolica across stand ages in the Mu Us Desert

Zhao

Guo

Gao

et al. 2020

Ecology and Evolution

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Root‐associated fungi (RAF) are an important factor affecting the host's growth, and their contribution to Pinus sylvestris var. mongolica plantation decline is substantial. Therefore, we selected three age groups of P. sylvestris plantations (26, 33, and 43 years), in the Mu Us Desert, to characterize the community structure and functional groups of RAF, identified by Illumina high‐throughput sequencing and FUNGuild platform, respectively. The effects of soil properties and enzyme activities on fungal diversity and functional groups were also examined. The results indicated that (a) 805 operational taxonomic units of RAF associated with P. sylvestris belonged to six phyla and 163 genera. Diversity and richness were not significantly different in the three age groups, but community composition showed significant differences. Ascomycota and Basidiomycota dominated the fungal community, while Rhizopogon dominated in each plot. (b) The proportion of pathotrophs decreased with increasing age, while that of symbiotrophs increased sharply, which were mainly represented by ectomycorrhizal fungi. (c) Stand age and soil enzyme activity had a greater influence on fungal community composition than did soil properties, whereas environmental variables were not significantly correlated with fungal diversity and richness. Dynamics of fungal community composition and functional groups with the aging plantations reflected the growth state of P. sylvestris and were related to plantation degradation.

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Drivers of microbial community structure in forest soils

Cited by 183 publications

References 85 publications

Climatic impacts on the bacterial community profiles of cork oak soils

Climatic impacts on the bacterial community profiles of cork oak soils

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Community structure and functional group of root‐associated Fungi of Pinus sylvestris var. mongolica across stand ages in the Mu Us Desert

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