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Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography

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A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Forest Soil".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 15132

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Prof. Dr. Hui Li

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Guest Editor

Shenyang Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
Interests: aboveground-belowground interactions; climate change microbiology; microbial biogeography; soil microbial ecology; forest soil microorganisms

Prof. Dr. Yuguang Zhang

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Guest Editor

Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Key Laboratory of Biological Conservation of State Forestry Administration, Beijing 100091, China
Interests: human–wildlife conflicts; conservation biology; protected area management; landscape genetics; conservation genetics
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Dear Colleagues,

Forest ecosystems harbor a great diversity of soil microorganisms, however, soil microbes in forest ecosystems are not finely analyzed in comparison with agricultural and grassland systems. In forest ecosystem, aboveground plant community dynamics are closely linked with soil microorganisms. Plants provide the organic carbon required by the soil microorganisms, and the microbes in turn breaks down dead wood materials and regulates plant growth and community dynamics by supplying available soil nutrients. Particularly, plants structure their own fitness and competitiveness through recruiting and cooperating with soil microbes, such as symbiotic or pathogenic hostile species. Forest ecosystems are more sensitive to climate change, due to the high soil organic carbon content. How soil microorganisms would respond to climate change (for instance, drought and warming), and how these change would associate with the variations in plant community dynamics, is still not clear. In comparison with plant and animals, the biogeography of soil microorganisms has received less attention. The distribution of soil microbes and their potential associations with plants distribution is a hot topic in ecology. We encourage studies from all these fields, including plant-microbes interactions, climate change microbiology, and microbial biogeography, to contribute to this Special Issue in order to deepen our understanding on the ecological linkages between the aboveground and belowground biota in forest ecosystem.

Prof. Dr. Hui Li
Prof. Dr. Yuguang Zhang
Guest Editors

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Keywords

climate change microbiology
biogeocycling
aboveground-belowground interactions
microbial biodiversity
microbial biogeography
microbial community assembly

Published Papers (8 papers)

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Research

17 pages, 4957 KiB

Open AccessArticle

Molecular Ecological Network Structure and Potential Function of the Bacterial Community in the Soil Profile under Indigenous Tree Plantations in Subtropical China

by Lin Qin, Yufeng Wang, Angang Ming, Shouhong Xi, Zhirou Xiao, Jinqian Teng and Ling Tan

Forests 2023, 14(4), 803; https://doi.org/10.3390/f14040803 - 14 Apr 2023

Cited by 1 | Viewed by 1248

Abstract

The soil profile is a strong and complex physicochemical gradient that greatly affects bacterial community structure and function between soil layers. However, little is known about molecular ecological network structure and bacterial community function under differing soil profiles in planted forests. Four typical native tree species (Pinus massoniana Lamb., Castanopsis hystrix Miq., Mytilaria laosensis Lec., and Michelia macclurei Dandy) plantations were selected from subtropical China as the research object. We evaluated molecular ecological network structure as well as potential function of the soil bacterial community at different soil depths (0–20, 20–40, and 40–60 cm) within native tree plantations. Our results showed that (1) compared to the topsoil (0–20 cm), the bacterial molecular ecological network scale increased within the middle layer (20–40 cm) and the subsoil (40–60 cm), and the interaction between species was stronger; (2) module hubs and connectors were the key bacterial groups in each soil layer and increased with increasing soil depth; (3) the dominant functional groups of the bacterial communities in each soil layer were chemoheterotrophy, aerobic chemoheterotrophy, cellulolysis, ureolysis, nitrogen fixation, and nitrate reduction, and they were related to soil carbon and nitrogen cycling; and (4) the different molecular ecological network structures along with relative bacterial functional group abundances among diverse soil layers were mainly affected by soil organic carbon (SOC), NO₃⁻-N, NH₄⁺-N, available phosphorus (AP), and total phosphorus (TP). Our study provides a theoretical foundation for bacterial community structure together with function within soil profiles of native tree plantations in subtropical regions. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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16 pages, 3703 KiB

Open AccessArticle

Stoichiometric Soil Microbial and Enzymatic Characteristics under Three Different Plantation Types in China’s Luya Mountain

by Xuerong Wang, Mengyao Zheng, Yue Zhang, Ying Chen, Lijuan Zhao, Baofeng Chai and Tong Jia

Forests 2023, 14(3), 558; https://doi.org/10.3390/f14030558 - 12 Mar 2023

Cited by 1 | Viewed by 1339

Abstract

It is important to maintain soil ecosystem function and ecological balance stability. This study uses ecological stoichiometry to ascertain relational constraints of soil nutrient (i.e., carbon (C), nitrogen (N), phosphorus (P), etc.) cycling mechanisms and associated ecological balance characteristics in China’s temperate Luya Mountain Nature Reserve. To clarify changes and driving factors associated with soil and extracellular enzyme stoichiometry under different plantation types in July 2021, we analyzed soil nutrient, soil extracellular enzyme, and soil microbial stoichiometry characteristics and their key influencing factors in a Picea asperata Mast. forest, a Caragana jubata (Pall.) Poir. shrubland, and a Carex lanceolata Boott meadow in this reserve. Results revealed significant differences in soil physical and chemical properties, microbial biomass, soil extracellular enzyme activity, and stoichiometry among these different plantation types. Compared to the shrubland and forest plantations, meadow plantation soil was more severely C restricted while that of all three plantations was more N restricted. The main influencing soil stoichiometric ratios were total carbon (TC), total nitrogen (TN), total phosphorus (TP), ammonium (NH₄⁺-N), soil water content (SWC), β-glucosidase, and microbial C, N, and P biomass. Effects associated with soil N:P, enzymatic N:P, enzymatic C:P, microbial C:N, microbial N:P, and microbial C:P ratios were important for bacterial and fungal community soil structure. This study provides a scientific basis to explicate microbial and regulatory effects of soil extracellular enzyme stoichiometry under different plantation types in one of China’s best preserved and most concentrated natural secondary forests. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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16 pages, 2496 KiB

Open AccessEditor’s ChoiceArticle

Linking Bacterial Rhizosphere Communities of Two Pioneer Species, Brachystegia boehmii and B. spiciformis, to the Ecological Processes of Miombo Woodlands

by Camilo B. S. António, Chinedu Obieze, João Jacinto, Ivete S. A. Maquia, Tara Massad, José C. Ramalho, Natasha S. Ribeiro, Cristina Máguas, Isabel Marques and Ana I. Ribeiro-Barros

Forests 2022, 13(11), 1840; https://doi.org/10.3390/f13111840 - 04 Nov 2022

Cited by 1 | Viewed by 1850

Abstract

Miombo is the most extensive ecosystem in southern Africa, being strongly driven by fire, climate, herbivory, and human activity. Soils are major regulating and supporting services, sequestering nearly 50% of the overall carbon and comprising a set of yet unexploited functions. In this study, we used next-generation Illumina sequencing to assess the patterns of bacterial soil diversity in two pioneer Miombo species, Brachystegia boehmii and Brachystegia spiciformis, along a fire gradient, in ferric lixisol and cambic arenosol soils. In total, 21 phyla, 51 classes, 98 orders, 193 families, and 520 genera were found, revealing a considerably high and multifunctional diversity with a strong potential for the production of bioactive compounds and nutrient mobilization. Four abundant genera characterized the core microbiome among plant species, type of soils, or fire regime: Streptomyces, Gaiella, Chthoniobacter, and Bacillus. Nevertheless, bacterial networks revealed a higher potential for mutualistic interactions and transmission of chemical signals among phylotypes from low fire frequency sites than those from high fire frequency sites. Ecological networks also revealed the negative effects of frequent fires on the complexity of microbial communities. Functional predictions revealed the core “house-keeping” metabolisms contributing to the high bacterial diversity found, suggesting its importance to the functionality of this ecosystem. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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17 pages, 4803 KiB

Open AccessArticle

Interkingdom Plant–Soil Microbial Ecological Network Analysis under Different Anthropogenic Impacts in a Tropical Rainforest

by Jingjing Yu, Wei Cong, Yi Ding, Lixiao Jin, Jing Cong and Yuguang Zhang

Forests 2022, 13(8), 1167; https://doi.org/10.3390/f13081167 - 23 Jul 2022

Cited by 3 | Viewed by 1650

Abstract

Plants and their associated soil microorganisms interact with each other and form complex relationships. The effects of slash-and-burn agriculture and logging on aboveground plants and belowground microorganisms have been extensively studied, but research on plant–microbial interkingdom ecological networks is lacking. In this study, using old growth forest as a control, we used metagenomic data (ITS and 16S rRNA gene amplified sequences) and plant data to obtain interdomain species association patterns for three different soil disturbance types (slash-and-burn, clear cutting and selective cutting) in a tropical rainforest based on interdomain ecological network (IDEN) analysis. Results showed that the soil bacterial–fungal and plant–microbe ecological networks had different topological properties among the three forest disturbance types compared to old growth forest. More nodes, links, higher modularity and negative proportion were found in the selective cutting stand, indicating higher stability with increasing antagonistic relationships and niche differentiation. However, the area of slash-and-burn forest yield opposite results. Network module analysis indicated that different keystone species were found in the four forest types, suggesting alternative stable states among them. Different plant species had more preferential associations with specific fungal taxa than bacterial taxa at the genus level and plant–microbe associations lagged behind bacterial–fungal associations. Overall, compared with old growth forests, the bacterial–fungal and plant–microbe ecological networks in the slash-and-burn and clear cutting stands were simpler, while the network in the selective cutting stand was more complex. Understanding the relationships between aboveground plants and belowground microorganisms under differing disturbance patterns in natural ecosystems will help in better understanding the surrounding ecosystem functions of ecological networks. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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16 pages, 2981 KiB

Open AccessArticle

The Effects of Biochar on Microbial Community Composition in and Beneath Biological Soil Crusts in a Pinus massoniana Lamb. Plantation

by Jinping Wang, Rongzhen Huang, Liqin Zhu, Hongzhi Guan, Lijing Lin, Huanying Fang, Mengjia Yang, Shaohui Ji, Xianhua Zou and Xin Li

Forests 2022, 13(7), 1141; https://doi.org/10.3390/f13071141 - 20 Jul 2022

Cited by 8 | Viewed by 1909

Abstract

Biological soil crusts (BSCs) hold promise for reducing soil erosion in subtropical forest plantations, and microorganisms profoundly affect the formation and development of BSCs. The effects of biochar as a soil conditioner on the diversity and structure of soil microbial communities in BSCs are largely unknown. Therefore, our aim was to determine how biochar might improve microbial community composition and BSC function. Herein, a field experiment was conducted in a P. massoniana plantation; the addition of biochar was the treatment, and no biochar addition was the control (CK). Soil microbial communities associated with moss BSCs (in and beneath BSCs) with and without the addition of biochar were analyzed by Illumina sequencing technology. The results showed that Acidobacteria (28.35%), Proteobacteria (22.53%), Actinobacteria (17.41%), and Chloroflexi (16.74%) were the dominant bacterial phyla, whereas Basidiomycota (70.00%) and Ascomycota (22.76%) were the dominant fungal phyla in BSCs. The soil bacterial and fungal OTU number and richness in BSCs were higher than those beneath BSCs. The relative abundances of Acidobacteria, Chloroflexi, and Basidiomycota were higher in BSCs than beneath BSCs, whereas the relative abundances of Actinobacteria, Firmicutes, Ascomycota, and Chytridiomycota showed the opposite trend. Beneath BSCs, biochar addition increased the soil bacterial OTU number and richness (ACE index and Chao1) but decreased the soil fungal OTU number and richness. Biochar had little effect on soil microbial community structures in BSCs; however, beneath BSCs, it significantly increased the relative abundances of Acidobacteria, Chloroflexi, and Basidiomycota and significantly decreased the relative abundances of Actinobacteria, Firmicutes, Ascomycota, and Chytridiomycota. Biochar-induced changes in soil microbial communities were related to soil environmental factors, especially urease activity, organic matter content, pH, total nitrogen content, and sucrase activity. We demonstrated the different effects of biochar on soil microbial communities in and beneath the BSCs of subtropical forest plantations; these findings provided new insights into soil stabilization with BSCs below the forest canopy in subtropical regions. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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19 pages, 5705 KiB

Open AccessFeature PaperArticle

Soil Type Influences Rhizosphere Bacterial Community Assemblies of Pecan Plantations, a Case Study of Eastern China

by Yujie Tang, Junping Liu, Jiashu Bao, Guolin Chu and Fangren Peng

Forests 2022, 13(3), 363; https://doi.org/10.3390/f13030363 - 22 Feb 2022

Cited by 6 | Viewed by 1822

Abstract

The rhizosphere microbiome is closely related to forest health and productivity. However, whether soil type affects pecan (Carya illinoinensis) rhizosphere microbiomes is unclear. We aimed to explore the diversity and structural characteristics of rhizosphere bacteria associated with pecan plantations grown in three soil types (Luvisols, Cambisols, Solonchaks) in Eastern China and analyze their potential functions through high-throughput sequencing. The results showed that the diversity and community structure of rhizosphere bacteria in pecan plantations were significantly affected by soil type and the pH, available phosphorus content, electrical conductivity, soil moisture, and ammonium nitrogen contents were the main factors. At the phylum level, the rhizosphere bacterial community composition was consistent, mainly included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. At the family level, the pecan plantations formed different rhizosphere enriched biomarkers due to the influence of soil type, with functional characteristics such as plant growth promotion and soil nutrient cycling. In addition, there existed low abundance core species such as Haliangiaceae, Bryobacteraceae, and Steroidobacteraceae. They played important roles in the rhizosphere environments through their functional characteristics and community linkages. Overall, this study provides a basis for the study of the rhizosphere microbiome in different soil types of pecan plantations, and plays an important role in the sustainable management of forest soil. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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14 pages, 8752 KiB

Open AccessArticle

Secondary Succession in the Tropical Lowland Rainforest Reduced the Stochasticity of Soil Bacterial Communities through the Stability of Plant Communities

by Xuan Hu, Qi Shu, Zean Shang, Wen Guo and Lianghua Qi

Forests 2022, 13(2), 348; https://doi.org/10.3390/f13020348 - 18 Feb 2022

Cited by 2 | Viewed by 1694

Abstract

The effects of natural succession on plant and soil bacterial communities were previously established, but changes in plant and soil bacterial communities and their response to soil properties are not well characterized in different stages of secondary forest succession, especially in tropical regions with endemic plant species. We investigated the dynamics of plant communities, soil properties and the structure of soil bacterial communities at sites representing 33 (early successional stage), 60 (early-mid successional stage) and 73 (mid successional stage) years of secondary succession in the tropical lowland rainforest of Hainan, China, by using16S rRNA high-throughput sequencing. From the perspective of plant composition, the number of families, genera and species were increasing along with the progress of succession. Additionally, the changes in the ranking of important values along with the progress of the forest succession were consistent with the niche width calculated by the previous stage of the plant community. The results of niche overlap, Pearson’s correlation and Spearman’s rank correlation coefficients and significance indicated that in the early stage of succession, tree species did not fully utilize environmental resources. Then, as time went by, the number of negative correlations of plants in the early-mid stage was more than that in the mid stage of succession. Significant differences were found in the species richness of soil microorganisms among the three successional stages. Nutrient contents in early successional stage rainforests were less abundant than in early-mid and mid forest soils. The influence of soil nutrient concentration, particularly N and P content, on soil bacterial composition at the phylum level was larger in the early-mid stage than in the mid stage. The stochasticity of the soil bacterial community at the early successional stage of the rainforest was significantly higher than that at mid stage. Overall, as the diversity of plant communities increased, the competition decreased, the soil nutrient content changed and the stochasticity of soil bacterial communities decreased as a result of forest succession. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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13 pages, 2280 KiB

Open AccessArticle

Short-Term Effects of Cover Grass on Soil Microbial Communities in an Apple Orchard on the Loess Plateau

by Pan Wan and Ruirui He

Forests 2021, 12(12), 1787; https://doi.org/10.3390/f12121787 - 16 Dec 2021

Cited by 4 | Viewed by 2105

Abstract

Grass cover may improve soil environmental conditions in apple orchards. However, the mechanisms for how the soil microbial community changes after cover grass treatments are not well understood. In this study, we analyzed soil properties, microbial community diversity and composition in an apple orchard after being covered with native wild grasses for 3 years on the Loess Plateau, China. The ratios of cover grass were 0% (no cover, NC), 20% (low-intensity cover, LIC), 40% (moderate-intensity cover, MIC₁), 60% (moderate-intensity cover, MIC₂) and 80% (high-intensity cover, HIC). Meanwhile, the relationships between soil nutrients, cover grass properties, and microbial communities was analyzed by redundancy analysis and Pearson correlations. The results showed that cover grass altered the bacterial community composition, and significant changes at the phylum level were mainly caused by Proteobacteria, Bacteroidetes and Chloroflexi. Compared with NC, the abundance of Proteobacteria was lower in LIC, and the abundance of Bacteroidetes was lower in LIC, MIC₁ and MIC₂, while that of Chloroflexi was higher in LIC. LIC and MIC₁ were the only cover grass intensities that altered the soil fungal community composition; there were no significant differences at the phylum level. The changes in the soil microbial community at the given phyla may be related to the change in soil available nitrogen content caused by cover grass. Here, we demonstrate that cover grass changed the soil microbial community, and the changes may be attributed to the given phyla in the bacterial community; soil copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) were found to be at lower abundance in the low-intensity cover grass. Full article

(This article belongs to the Special Issue Soil Microorganisms in Forests: Biodiversity, Ecological Function, and Biogeography)

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