Use of soil enzyme activities to assess the recovery of soil functions in abandoned coppice forest systems

Recover of Soil Microbial Community Functions in Beech and Turkey Oak Forests After Coppicing Interventions

Forest management influences the occurrence of tree species, the organic matter input to the soil decomposer system, and hence, it can alter soil microbial community and key ecosystem functions it performs. In this study, we compared the potential effect of different forest management, coppice and high forest, on soil microbial functional diversity, enzyme activities and chemical-physical soil properties in two forests, turkey oak and beech, during summer and autumn. We hypothesized that coppicing influences soil microbial functional diversity with an overall decrease. Contrary to our hypothesis, in summer, the functional diversity of soil microbial community was higher in both coppice forests, suggesting a resilience response of the microbial communities in the soil after tree cutting, which occurred 15-20 years ago. In beech forest under coppice management, a higher content of soil organic matter (but also of soil recalcitrant and stable organic carbon) compared to high forest can explain the higher soil microbial functional diversity and metabolic activity. In turkey oak forest, although differences in functional diversity of soil microbial community between management were observed, for the other investigated parameters, the differences were mainly linked to seasonality. The findings highlight that the soil organic matter preservation depends on the type of forest, but the soil microbial community was able to recover after about 15 years from coppice intervention in both forest ecosystems. Thus, the type of management implemented in these forest ecosystems, not negatively affecting soil organic matter pool, preserving microbial community and potentially soil ecological functions, is sustainable in a scenario of climate change.

Phytobial remediation advances and application of omics and artificial intelligence: a review

Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain

Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality.

IMPORTANCE

The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation

As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.

Biochar loaded with bacteria enhanced Cd/Zn phytoextraction by facilitating plant growth and shaping rhizospheric microbial community

Biochar and metal-tolerant bacteria have been widely used in the remediation of heavy metal contaminated soil. However, the synergistic effect of biochar-functional microbes on phytoextraction by hyperaccumulators remains unclear. In this study, the heavy metal-tolerant strain Burkholderia contaminans ZCC was selected and loaded on biochar to produce biochar-resistant bacterial material (BM), and the effects of BM on Cd/Zn phytoextraction by Sedum alfredii Hance and rhizospheric microbial community were explored. The results showed that, BM application significantly enhanced the Cd and Zn accumulation of S. alfredii by 230.13% and 381.27%, respectively. Meanwhile, BM alleviated metal toxicity of S. alfredii by reducing oxidative damage and increasing chlorophyll and antioxidant enzyme activity. High-throughput sequencing revealed that BM significantly improved soil bacterial and fungal diversity, and increased the abundance of genera with plant growth promoting and metal solubilizing functions such as Gemmatimonas, Dyella and Pseudarthrobacter. Co-occurrence network analysis showed that BM significantly increased the complexity of the rhizospheric bacterial and fungal network. Structural equation model analysis revealed that soil chemistry property, enzyme activity and microbial diversity contributed directly or indirectly to Cd and Zn extraction by S. alfredii. Overall, our results suggested that biochar- B. contaminans ZCC was able to enhance the growth and Cd/Zn accumulation by S. alfredii. This study enhanced our understanding on the hyperaccumulator-biochar-functional microbe interactions, and provided a feasible strategy for promoting the phytoextraction efficiency of heavy metal contaminated soils.

Soil Nutrients, Enzyme Activities, and Microbial Communities along a Chronosequence of Chinese Fir Plantations in Subtropical China

Forests undergo a long-term development process from young to mature stages, yet the variations in soil nutrients, enzyme activities, microbial diversity, and community composition related to forest ages are still unclear. In this study, the characteristics of soil bacterial and fungal communities with their corresponding soil environmental factors in the young, middle, and mature stages (7, 15, and 25-year-old) of Chinese fir plantations (CFP) in the subtropical region of China were investigated in 2021. Results showed that the alpha diversity indices (Chao1 and Shannon) of soil bacteria and fungi were higher in 15 and 25-year-old stands than in 7-year-old stand of CFP, while the soil pH, soil water content, soil organic carbon, total nitrogen, total phosphorus, sucrase, urease, acid phosphatase, catalase, and microbial biomass carbon, nitrogen, and phosphorus showed higher in 7-year-old stand than other two stands of CFP. The nonmetric multidimensional scaling analysis revealed that the soil microbial species composition was significantly different in three stand ages of CFP. The redundancy and canonical correspondence analysis indicated that the soil urease and microbial biomass nitrogen were the main factors affecting soil bacterial and fungal species composition. Our findings suggested that soil microbial diversity and community structure were inconsistent with changes in soil nutrients and enzyme activities during CFP development, and enhancing stand nurturing and soil nutrient accumulation in the mid-development stage were beneficial to the sustainable management of CFP.

Links among Microbial Communities, Soil Properties and Functions: Are Fungi the Sole Players in Decomposition of Bio-Based and Biodegradable Plastic?

The incomplete degradation of bio-based and biodegradable plastics (BBPs) in soils causes multiple threats to soil quality, human health, and food security. Plastic residuals can interact with soil microbial communities. We aimed to link the structure and enzyme-mediated functional traits of a microbial community composition that were present during poly (butylene succinate-co-butylene adipate (PBSA) decomposition in soil with (PSN) and without (PS) the addition of nitrogen fertilizer ((NH₄)₂SO₄). We identified bacterial (Achromobacter, Luteimonas, Rhodanobacter, and Lysobacter) and fungal (Fusarium, Chaetomium, Clonostachys, Fusicolla, and Acremonium) taxa that were linked to the activities of ß-glucosidase, chitinase, phosphatase, and lipase in plastic-amended soils. Fungal biomass increased by 1.7 and 4 times in PS and PSN treatment, respectively, as compared to non-plastic amended soil. PBSA significantly changed the relationships between soil properties (C: N ratio, TN, and pH) and microbial community structure; however, the relationships between fungal biomass and soil enzyme activities remained constant. PBSA significantly altered the relationship between fungal biomass and acid phosphatase. We demonstrated that although the soil functions related to nutrient cycling were not negatively affected in PSN treatment, potential negative effects are reasoned by the enrichment of plant pathogens. We concluded that in comparison to fungi, the bacteria demonstrated a broader functional spectrum in the BBP degradation process.

Pecan agroforestry systems improve soil quality by stimulating enzyme activity

BACKGROUND

Forest and plantation intercropping are efficient agroforestry systems that optimize land use and promote agroforestry around the world. However, diverse agroforestry systems on the same upper-plantation differently affect the physical and chemical properties of the soil.

METHODS

The treatments for this study included a single cultivation (CK) pecan control and three agroforestry systems (pecan + Paeonia suffruticosa + Hemerocallis citrina, pecan + Paeonia suffruticosa, and pecan + Paeonia lactiflora). Soil samples were categorized according to the sampling depth (0-20 cm, 20-40 cm, 40-60 cm).

RESULTS

The results demonstrated that the bulk density (BD) of soil under the pecan agroforestry system (PPH and PPL) was reduced by 16.13% and 7.10%, respectively, and the soil moisture content (MC) and total soil porosity (TPO) increased. Improvements in the physical properties of the soil under the PPS agroforestry system were not obvious when compared with the pecan monoculture. The soil total phosphorus (TP), total nitrogen (TN), available potassium (AK), and total carbon (TC) increased significantly, while the soil urease (S-UE), alkaline phosphatase (S-AKP), and 1,4-β-N-acetylglucosamines (S-NAG) enzyme activity also increased significantly, following agroforestry. Overall, the pecan agroforestry system significantly improved the physical properties of the pecan plantation soil, enriched the soil nutrients, and increased the activity of soil enzymes related to TC, TN, and TP cycles.

Study of pollutant accumulation characteristics and microbial community impact at three bioretention facilities

In this paper, three bioretention facilities (BT, RG1-A, and RG1-B) were selected for on-site testing and experimental analysis. Of which, BT is a roadside bioretention tank with layered filler, while RG1-A and RG1-B are rain gardens with conventional filler (Bioretention soil media, BSM) and modified filler (BSM+10% Water treatment residuals,WTR), respectively. The effect of pollutant accumulation on the soil microbial community structure in the facilities, and the risk of heavy metal contamination over several years of bioretention facility operation were studied. Results showed that the water quality pollutant load reduction in BT was fluctuating. This is related  to the poor water quality of road stormwater flowing into BT and the facility filler. Because RG1-B uses modified filler, RG1-B was more effective than RG1-A in regulating water quality and quantity; the changes in soil physical and chemical properties in BT, RG1-A, and RG1-B were influenced by external factors. Next, BT was at high risk of heavy metal contamination than other facilities. The microbial community structure of the facility had the following characteristics: at the phylum level, Proteobacteria was the dominant phylum in the bioretention facility, accounting for 29-45%; and at the genus level, Blastocatella was the dominant phylum, and the relative abundance in situ was higher than that in the bioretention facility. The results of the correlation analysis combining filler environmental factors and microbial community structure indicated that SMC was a highly influential factor among the three facilities.

Effect of biodegradable film mulching on crop yield, soil microbial and enzymatic activities, and optimal levels of irrigation and nitrogen fertilizer for the Zea mays crops in arid region

Biodegradable film mulching (BM) is considered as the best alternative to plastic film mulching (PM) since it can prevent pollution caused due to plastic residues. However, the differences in soil microbial biomass and enzymatic activities between BM and PM, especially for different soil water and nitrogen contents remain ambiguous. In this study, the effects of BM, PM, and no film mulching (NM) on soil microbial biomass C (C_mic), N (N_mic), soil enzymes, and soil C/N ratio in a cornfield were evaluated using experimental data from 2018 and 2019. Additionally, different irrigation depths (30 mm, 22.5 mm, and 15 mm) and N-fertilizer application levels (280 kg ha^-1 and 210 kg ha^-1) were used in BM. The experimental results demonstrated no apparent differences between the C_mic, N_mic, and soil enzymes between BM and PM in the early stage (elongation stage), but these values under BM were significantly lower than that of PM in the middle stage of crop growth (tasseling and filling stages). Soil sucrase, catalase, and urease under PM were increased by 20.2%, 0.6%, and 12.0%, respectively, compared to BM. The analysis of C_mic, N_mic, soil enzymes, and crop yield under different irrigation and N-fertilizer application levels demonstrated the preponderance of BM_{22.5, 280,} showing the highest yield of 14,110.1 kg ha^-1 and NUE of 61.7.

Conversion of cropland to natural vegetation boosts microbial and enzyme activities in soil

The trends of enzyme activities and litter chemistry after abandonment of arable soil and succession of natural vegetation were studied in a deciduous forest zone (Moscow region, Russia). The Luvic Phaeozem chronosequence included an arable field, 3 fields with increasing abandonment periods (7, 11, 35 years), and the soil under natural forest as a reference site (never used for cropland). The activities of four hydrolytic enzymes (β-glucosidase, cellobiohydrolase, β-galactosidase, chitinase) in the topsoil (0-5 cm) were compared with chemical functional groups of plant litter identified by ¹³C NMR spectra. The total enzyme activity increased 5-fold during 35 years of postagricultural restoration of arable soil. The share of C-cycle enzymes with "narrower" substrate specificity (cellobiohydrolase and chitinase) increased during 35 years from 19% to 42% of the total enzyme pool. We explain this gain by the increase in the diversity and recalcitrance of organic compounds in the plant litter from cropland to natural forest. Aromaticity index of plant litter built up remarkably: from 0.11 in the young abandoned land to 0.14-0.15 in the 35-year abandoned land and the reference site. The share of enzymes with a "narrower" substrate specificity correlated closely with the portions of aryl C, O-aryl C, and carbonyl C functional groups in plant litter. Accordingly, the succession of natural vegetation on abandoned cropland leads to strong diversification of the plant litter composition and a corresponding production of soil enzymes with "narrower" substrate specificity.

Effect of perfluorooctanoic acid on microbial activity in wheat soil under different fertilization conditions

Perfluorooctanoic acid (PFOA) is an emerging persistent organic pollutant which has been identified at significant levels in soils. Existed ecotoxicological studies have mainly employed earthworms to evaluate the toxicity of PFOA. However, little information do we know about the toxicity of PFOA regarding soil microorganisms. Accordingly, the adverse effects of PFOA on microbial activity in a wheat soil under four fertilization treatments were investigated in this study. The microcalorimetric results revealed that the toxicity of PFOA on soil microbial activity in four treatments followed a descending sequence: Control (no fertilization), NK (no P fertilizer, but N and K fertilizers were used), PK (no N fertilizer, but P and K fertilizers were used), and NPK (N, P and K fertilizers were used). The soil sample with higher available P content had higher resistant to PFOA. There were significant differences in urease activity and alkaline phosphatase activity among the four fertilization treated soils. Molecular modeling studies clearly demonstrated that the binding of PFOA with alkaline phosphatase was more stable than with urease through electrostatic interaction, van der Waals force, and hydrogen bonds. These results are expected to provide more comprehensive information in toxicity of PFOA in soil environment.

Soil protein as a potential antimicrobial agent against methicillin -resistant Staphylococcus aureus

Recently, the interest is increasing to find alternatives to replace the usage of antibiotics since their massive and improper usage enhance the antibiotic resistance in human pathogens. In this study, for the first time we showed that the soil proteins have very high antibacterial activity (98% of growth inhibition) against methicillin resistant Staphylococcus aureus (MRSA), one of the most threatening human pathogens. We found that the protein extract (C3) from the forest with past intensive management showed higher antibacterial activity than that of unmanaged forest. The MIC and IC₅₀ were found to be 30 and 15.0 μg protein g^-1 dry soil respectively. C3 was found to kill the bacteria by cell wall disruption and genotoxicity which was confirmed by optical and fluorescent microscopy and comet assay. According to qPCR study, the mecA (the antibiotic resistant gene) expression in MRSA was found to be down-regulated after C3 treatment. In contrast, C3 showed no hemolytic toxicity on human red blood cells which was confirmed by hemolytic assay. According to ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), 144 proteins were identified in C3 among which the majority belonged to Gram negative bacteria (45.8%). Altogether, our results will help to develop novel, cost-effective, non-toxic and highly efficient antibacterial medicines from natural sources against antibiotic resistant infections.

Sustainable soil use and management: An interdisciplinary and systematic approach

Soil is a key component of Earth's critical zone. It provides essential services for agricultural production, plant growth, animal habitation, biodiversity, carbon sequestration and environmental quality, which are crucial for achieving the United Nations' Sustainable Development Goals (SDGs). However, soil degradation has occurred in many places throughout the world due to factors such as soil pollution, erosion, salinization, and acidification. In order to achieve the SDGs by the target date of 2030, soils may need to be used and managed in a manner that is more sustainable than is currently practiced. Here we show that research in the field of sustainable soil use and management should prioritize the multifunctional value of soil health and address interdisciplinary linkages with major issues such as biodiversity and climate change. As soil is the largest terrestrial carbon pool, as well as a significant contributor of greenhouse gases, much progress can be made toward curtailing the climate crisis by sustainable soil management practices. One identified option is to increase soil organic carbon levels, especially with recalcitrant forms of carbon (e.g., biochar application). In general, soil health is primarily determined by the actions of the farming community. Therefore, information management and knowledge sharing are necessary to improve the sustainable behavior of practitioners and end-users. Scientists and policy makers are important actors in this social learning process, not only to disseminate evidence-based scientific knowledge, but also in generating new knowledge in close collaboration with farmers. While governmental funding for soil data collection has been generally decreasing, newly available 5G telecommunications, big data and machine learning based data collection and analytical tools are maturing. Interdisciplinary studies that incorporate such advances may lead to the formation of innovative sustainable soil use and management strategies that are aimed toward optimizing soil health and achieving the SDGs.

Changes in Soil Microbial Biomass, Community Composition, and Enzyme Activities After Half-Century Forest Restoration in Degraded Tropical Lands

Soil carbon (C) sequestration and stabilization are determined by not only the C input to the soil but also the decomposition rate of soil organic matter (SOM), which is mainly mediated by soil microbes. Afforestation, an effective practice to restore forests from degraded or bare lands, may alter soil microbial properties, and thus soil C and nitrogen (N) dynamics. The aim of this study was to investigate the impacts of different afforestation strategies on soil microbial compositions and activities after afforestation for half a century. Soil samples were collected from two afforested sites (i.e., a restored secondary forest (RSF) and a managed Eucalyptus forest (MEP)) and two reference sites (i.e., a nearby undisturbed forest (UF), representing the climax vegetation and a bare land (BL), representing the original state before restoration) in south China. We quantified the soil microbial biomass, microbial community compositions, and activities of nine extracellular enzymes at different soil depths and in different seasons. Results showed that the soil microbial biomass, all the main soil microbial groups, and the activities of all extracellular enzymes were significantly increased after afforestation compared to the BL sites, while the ratios of fungi/bacteria (F/B), specific enzyme activities, and the ecoenzymatic stoichiometry were significantly decreased regardless of the season and soil depth. Between the two afforested sites, these microbial properties were generally higher in the RSF than MEP. However, the microbial properties in the RSF were still lower than those in the UF, although the differences varied with different seasons, soil depths, and microbial groups or enzymes. Our findings demonstrated that afforestation might significantly improve microbial properties. Afforestation is more effective in mixed-species plantation than in the monoculture Eucalyptus plantation but needs a much longer time to approach an equivalent level to the primary forests.