Dynamics of Soil Bacterial and Fungal Communities During the Secondary Succession Following Swidden Agriculture IN Lowland Forests

Mycobiome analysis of leaf, root, and soil of symptomatic oil palm trees (Elaeis guineensis Jacq.) affected by leaf spot disease

Recently, attention has been shifting toward the perspective of the existence of plants and microbes as a functioning ecological unit. However, studies highlighting the impacts of the microbial community on plant health are still limited. In this study, fungal community (mycobiome) of leaf, root, and soil of symptomatic leaf-spot diseased (SS) oil palm were compared against asymptomatic (AS) trees using ITS2 rRNA gene metabarcoding. A total of 3,435,417 high-quality sequences were obtained from 29 samples investigated. Out of the 14 phyla identified, Ascomycota and Basidiomycota were the most dominant accounting for 94.2 and 4.7% of the total counts in AS, and 75 and 21.2% in SS, respectively. Neopestalotiopsis is the most abundant genus for AS representing 8.0% of the identified amplicons compared to 2.0% in SS while Peniophora is the most abundant with 8.6% of the identified amplicons for SS compared to 0.1% in AS. The biomarker discovery algorithm LEfSe revealed different taxa signatures for the sample categories, particularly soil samples from asymptomatic trees, which were the most enriched. Network analysis revealed high modularity across all groups, except in root samples. Additionally, a large proportion of the identified keystone species consisted of rare taxa, suggesting potential role in ecosystem functions. Surprisingly both AS and SS leaf samples shared taxa previously associated with oil palm leaf spot disease. The significant abundance of Trichoderma asperellum in the asymptomatic root samples could be further explored as a potential biocontrol agent against oil palm disease.

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

BACKGROUND

Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).

RESULTS

To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.

CONCLUSIONS

Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

Climax forest has a higher soil bacterial diversity but lower soil nutrient contents than degraded forests in temperate northern China

Bacteria are a crucial component of forest soil biodiversity and play an important role in numerous ecosystem processes. Here, we studied the patterns of soil bacterial community diversity and structure in a climax forest (Larix gmelinii; LG) compared with those in degraded forest ecosystems of four forest vegetation types (BD, Betula dahurica; BP, Betula platyphylla; QM, Quercus mongolica; and LGQM, a mixed coniferous-broadleaved forest composed of Larix gmelinii and Quercus mongolica) in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve in northern China, using Illumina MiSeq sequencing of 16 S rRNA genes. Soil physicochemical properties (pH, soil organic carbon = SOC, total nitrogen = TN, carbon/nitrogen = C/N, total phosphorous = TP, available nitrogen = AN, available phosphorous = AP) differed significantly (p < .05) among the five forests. SOC, C/N, TP, AN, and AP were highest in QM, whereas SOC was lowest in LGQM. Soil pH was lowest in BD and highest in LGQM. α diversity was highest in LG and lowest in QM. The soil bacterial community composition in the climax forest was significantly different from that in the four degraded forests (p < .05). The dominant bacterial phyla were Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Firmicutes, Chloroflexi, and Rokubacteria. The highest relative abundances of these phyla were: 30.7% for Acidobacteria in LGQM, 42.6% for Proteobacteria in LG, 17.6% for Verrucomicrobia in BD, 5.5% for Firmicutes in BP, and 6.9% for Actinobacteria in QM. The dominant bacterial genera across the five forest vegetation types were Bryobacter and some poorly characterized taxa (e.g., Candidatus_Udaeobacter and Candidatus_Solibacter). Redundancy analysis indicated that SOC, C/N, TP, AN, and AP were the main soil physicochemical properties that shaped the bacterial communities. Our study revealed distinct bacterial diversity and composition in the climax forest compared with values in degraded forests, suggesting that the biotic and abiotic factors associated with climax ecosystems play an important role in shaping soil bacterial community structure and thus biogeochemical functions. The results of this study contribute to a deeper understanding and better predictions of the network among belowground systems and of the functions and services of degraded forests compared with climax ecosystems.

Variation in Soil Bacterial and Fungal Community Composition at Different Successional Stages of a Broad-Leaved Korean Pine Forest in the Lesser Hinggan Mountains

Soil microorganisms are an integral part of the soil and are highly sensitive to environmental changes. The shift in plant community and soil properties following forest succession may cause differences in soil bacterial and fungal community composition. Some studies suggested following the succession of the community, the species composition tends to switch from r-strategy groups to k-strategy groups. However, generalization on the changing pattern has not been worked out. Three forests at an early-, intermediate-, and late-stage (ES, IS, LS) of the succession of broad-leaved Korean pine forest in the Lesser Hinggan Mountains were surveyed to study the variation in soil bacterial and fungal community composition as the succession proceeds. Soil microbial community composition and related soil factors were analyzed by systematic sampling. Significant differences in soil microbial community composition were detected between forests at different stages. The bacterial diversity increased, while the fungal diversity decreased (p < 0.05) from the early to the late successional forest. The fungi to bacteria ratio (F/B) and the (Proteobacteria + Bacteroidetes) to (Actinobacteria + Acidobacteria) ratio increased substantially with succession (p < 0.05). At the phylum level, Bacteroidetes, Ascomycota and Mortierellomycota were dominant in the ES forest, while Actinobacteria and Basidiomycota were prevalent in the LS forest. At the class level, Gammaproteobacteria, Acidobacteriia, Bacteroidia, Sordariomycetes and Mortierellomycetes were dominant in the ES forest, whereas Subgroup_6, Agaricomycetes, Geminibasidiomycetes and Tremellomycetes were dominant in the LS forest. Soil water content (SWC) and available phosphorus (AP) had significant effects on the bacterial community composition (p < 0.05). Soil organic carbon (SOC), total nitrogen (TN), the carbon–nitrogen ratio (C/N), total potassium (TK) and SWC had significant effects on the fungal community composition (p < 0.05). SOC and TN were positively correlated with r-strategy groups (p < 0.05) and were significantly negatively correlated with k-strategy groups (p < 0.05). Our results suggest that the soil bacterial and fungal community composition changed significantly in forests across the successional stages, and the species composition switched from r-strategy to k-strategy groups. The bacterial and fungal community diversity variation differed in forests across the successional stages. The changes in soil organic carbon and nitrogen content resulted in the shifting of microbial species with different ecological strategies.

Influence of Different Vegetation Types on Soil Physicochemical Parameters and Fungal Communities

This study assessed the effects of Betula dahurica (BD), Betula platyphylla (BP), Larix gmelinii (LG), Quercus mongolica (QM), and a mixed conifer–broadleaf forest composed of LG and QM (LGQM) on the soil physicochemical parameters and community structure of fungi in the Zhongyangzhan Black-billed Capercaillie Nature Reserve. Fungal community structures were characterized via ITS rRNA sequencing. The effects of soil parameters on the community structure of soil fungi were assessed by Pearson correlation analysis and redundancy analysis (RDA). LGQM exhibited lower C/N, available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP) compared with the QM broadleaf forest. The fungal Shannon and Simpson diversity indices were highest in BP, whereas LG exhibited the highest ACE index. The Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota fungal phyla were dominant across all vegetation types. Each of the different vegetation types studied herein exhibited a unique fungal community structure. The RDA results indicated that fungal community structures were primarily shaped by the total N, available N, and available P of soil. Our findings thus indicated that forests restored with different species of trees may exhibit variations in soil quality and characteristics despite sharing the same climate. Furthermore, broadleaved and coniferous forests exhibited a unique fungal community diversity and composition.