Distinct Successions of Common and Rare Bacteria in Soil Under Humic Acid Amendment – A Microcosm Study

Li, Pengfa; Liu, Jia; Jiang, Chunyu; Wu, Meng; Liu, Ming; Li, Zhongpei

doi:10.3389/fmicb.2019.02271

Cited by 43 publications

(29 citation statements)

References 78 publications

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“…Species with wider niche breadth are considered to be generalists which are less influenced by environmental factors because of higher environmental tolerances (49,50). In our study, habitat niche breadth of fungi continuously increased along with soil depth (Fig.…”

Section: Discussionmentioning

confidence: 60%

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

Dumbrell

et al. 2020

mSystems

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Fungi underpin almost all terrestrial ecosystem functions, yet our understanding of their community ecology lags far behind that of other organisms. Here, red paddy soils in subtropical China were collected across a soil depth profile, comprising 0-to-10-cm- (0-10cm-), 10-20cm-, and 20-40cm-deep layers. Using Illumina MiSeq amplicon sequencing of the internal transcribed spacer (ITS) region, distance-decay relationships (DDRs), and ecological models, fungal assemblages and their spatial patterns were investigated from each soil depth. We observed significant spatial variation in fungal communities and found that environmental heterogeneity decreased with soil depth, while spatial variation in fungal communities showed the opposite trend. DDRs occurred only in 0-10cm- and 10-20cm-deep soil layers, not in the 20-40cm layer. Our analyses revealed that the fungal community assembly in the 0-10cm layer was primarily governed by environmental filtering and a high dispersal rate, while in the deeper layer (20-40cm), it was primarily governed by dispersal limitation with minimal environmental filtering. Both environmental filtering and dispersal limitation controlled fungal community assembly in the 10-20cm layer, with dispersal limitation playing the major role. Results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Effectively, “everything is everywhere, but the environment selects,” although only in shallower soils that are easily accessible to dispersive fungal propagules. This work highlights that perceived drivers of fungal community assembly are dependent on sampling depth, suggesting that caution is required when interpreting diversity patterns from samples that integrate across depths. IMPORTANCE In this work, Illumina MiSeq amplicon sequencing of the ITS region was used to investigate the spatial variation and assembly mechanisms of fungal communities from different soil layers across paddy fields in subtropical China, and the results demonstrate the decreasing importance of environmental filtering and an increase in the importance of dispersal limitation in structuring fungal communities from shallower to deeper soils. Therefore, the results of this study highlight that perceived drivers of fungal community assembly are dependent on sampling depth and suggest that caution is required when interpreting diversity patterns from samples that integrate across depths. This is the first study focusing on assemblages of fungal communities in different soil layers on a relatively large scale, and we thus believe that this study is of great importance to researchers and readers in microbial ecology, especially in microbial biogeography, because the results can provide sampling guidance in future studies of microbial biogeography.

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Section: Discussionmentioning

confidence: 60%

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

Dumbrell

et al. 2020

mSystems

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“…Collectively, the results suggested the importance of the deterministic and stochastic processes that complementarily and simultaneously governed the bacterial community across the soil profiles. The abundant groups in the bacterial communities were further parsed to better understand the taxon-specific selection and dispersal mechanisms (27)(28)(29). In our opinion, the type of ecological processes structuring the assembly of the bacterial phyla was depth dependent.…”

Section: Discussionmentioning

confidence: 99%

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

et al. 2020

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Soil microbial community assembly is crucial for understanding the mechanisms of microbial communities that regulate ecosystem-level functioning. The relative contributions of stochastic and deterministic processes to microbial community assembly remain poorly defined, and major questions exist concerning the soil organic carbon (SOC) dynamics of microbial community assembly in deep soil. Here, the bacterial community assembly processes were explored across five soil profile depths (up to 80 cm) during a 15-year field experiment involving four fertilization regimes. We found that the bacterial community assembly was initially governed by deterministic selection in topsoil but was progressively structured by increasing stochastic dispersal with depth. The migration rate (m) and β-null deviation pattern supported the hypothesis of a relatively greater influence of dispersal in deep soil, which was correlated with bacterial community assembly by stochastic processes. These changes in the entire community assembly reflected consistent assembly processes of the two most dominant phyla, Acidobacteria and Chloroflexi. Structural equation modeling showed that soil features (pH and total phosphorus) and bacterial interactions (competition and network complexity) were significantly related to bacterial community assembly in the 0-to-10-cm and 10-to-20-cm layers. Partial Mantel tests, structural equation modeling, and random forest modeling consistently indicated a strong and significant correlation between bacterial community assemblages and SOC dynamics, implying that bacterial assembly processes would potentially suppress SOC metabolism and mineralization when the contributions of stochastic dispersal to communities increased in deeper layers. Our results have important implications for integrating bacterial community assembly processes into the predictions of SOC dynamics. IMPORTANCE We have provided a framework to better understand the mechanisms governing the balance between stochastic and deterministic processes and to integrate the shifts in community assembly processes with microbial carbon metabolism. Our study reinforced that environmental filtering and bacterial cooccurrence patterns influence the stochastic/deterministic continuum of soil bacterial community assembly and that stochasticity may act through deeper soil layers to influence carbon metabolism. Delineating theoretically the potential linkages between community assembly and SOC dynamics across a broad range of microbial systems represents an interesting topic for future research.

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“…In a long-term fertilization experiment, a rare soil bacterial community, rather than a dominant soil bacterial community, controlled multiple ecosystem functions [ 3 ]. Li et al (2019) observed distinct changes in rare and abundant bacteria in response to humic acid amendment [ 4 ]. Similarly, a previous study reported that different patterns were observed between rare and abundant taxa in oil-contaminated soils [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

Zeng

2021

Microorganisms

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High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

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Distinct Successions of Common and Rare Bacteria in Soil Under Humic Acid Amendment – A Microcosm Study

Cited by 43 publications

References 78 publications

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

Spatial Variation in Soil Fungal Communities across Paddy Fields in Subtropical China

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

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