Mar 2023, Volume 5 Issue 1

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    Ole G. Mouritsen
    Alexandre Jousset, Seon-Woo Lee

    Microbiome transplants have the potential to disrupt agriculture and medicine by transferring the microbial genetic pool (and hence capabilities) from one host to another. Yet, for this technology to become reality, we need to understand the drivers shaping the success of microbiome transplant. We highlight here recent findings by Dr. Gaofei Jiang and colleagues. Using disease suppression as a model function, they highlight the microbiome characteristics making a successful transplant possible. We see this study is a seminal work making microbiome transplant an informed process that will replace the current error-prone trial procedures. We anticipate that the insights may catalyse a paradigm shift in microbiome management in agriculture and medicine.

    Zhaoan Sun, Fanqiao Meng, Biao Zhu

    ● This study reviewed the contribution of carbonates to soil CO2 emissions.

    ● The contribution was on average 27% in calcareous soils.

    ● The contribution was affected by both biotic and abiotic factors.

    ● We proposed a new method of distinguishing three CO2 sources from calcareous soils.

    In calcareous soils, recent studies have shown that soil-derived CO2 originates from both soil organic carbon (SOC) decomposition and soil inorganic carbon (SIC) dissolution, a fact often ignored in earlier studies. This may lead to overestimation of the CO2 emissions from SOC decomposition. In calcareous soils, there is a chemical balance between precipitation and dissolution of CaCO3-CO2- HCO3, which is affected by soil environmental factors (moisture, temperature, pH and depth), root growth (rhizosphere effect) and agricultural measures (organic materials input, nitrogen fertilization and straw removal). In this paper, we first introduced the contribution of SIC dissolution to CO2 emissions from calcareous soils and their driving factors. Second, we reviewed the methods to distinguish two CO2 sources released from calcareous soils and quantify the 13C fractionation coefficient between SIC and SIC-derived CO2 and between SOC and SOC-derived CO2, and to partition three CO2 sources released from soils with plants and organic materials input. Finally, we proposed methods for accurately distinguishing three CO2 sources released from calcareous soils. This review helps to improve the accuracy of soil C balance assessment in calcareous soils, and also proposes the direction of further investigations on SIC-derived CO2 emissions responses to abiotic factors and agricultural measures.

    Hengyi Dai, Yajuan Zhuang, Erinne Stirling, Nanlin Liu, Bin Ma

    • Microfluidic technology promotes the development of soil bacteria research.

    • Microfluidics can achieve real time observation and analysis of microorganisms in controlled environments.

    • Microfluidics generally use optical and electrochemical methods to detect single cells combined with polymerase chain reaction (PCR) to realize high throughput gene detection on chips.

    • Microfluidics is mainly applied in chemotaxis, biofilm, antibiotic and horizontal gene transfer research of soil bacteria.

    Soil science is an inherently diverse and multidisciplinary subject that cannot develop further without the continuous introduction and promotion of emerging technologies. One such technology that is widely used in biomedicine and similar research fields, microfluidics, poses significant benefits for soil research; however, this technology is still underutilized in the field. Microfluidics offers unparalleled opportunities in soil bacterial cultivation, observation, and manipulation when compared to conventional approaches to these tasks. This review focuses on the use of microfluidics for bacteria research and, where possible, pulls from examples in the literature where the technologies were used for soil related research. The review also provides commentary on the use of microfluidics for soil bacteria research and discusses the key challenges researchers face when implementing this technology. We believe that microfluidic chips and their associated auxiliary technologies provide a prime inroad into the future of soil science research.

    Barak Dror, Edouard Jurkevitch, Eddie Cytryn

    ● The overall abundance of secondary metabolites-encoding genes in soil and root microbiomes is similar.

    ● Certain biosynthetic gene clusters (BGCs) are ubiquitous and more abundant in roots compared with soil.

    ● The majority of identified BGCs are potentially novel.

    Secondary metabolites (SMs) produced by soil bacteria, for instance antimicrobials and siderophores, play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health. Many SMs are non-ribosomal peptides and polyketides, assembled by non-ribosomal peptides synthetase (NRPS) and polyketide synthase (PKS) and encoded by biosynthetic gene clusters (BGCs). Despite their ecological importance, little is known about the occurrence and diversity of NRPs and PKs in soil. We extracted NRPS- and PKS-encoding BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB. We found that the overall abundance of NRPSs and PKSs is similar in both environments, however NRPSs and PKSs were significantly clustered between soil and root samples. Moreover, the majority of identified sequences were unique to either soil- or root-associated datasets and had low identity to known BGCs, suggesting their novelty. Overall, this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes, and indicates presence of specific SMs, which may play a role in inter- and intra-bacterial interactions in root ecosystems.

    Gaidi Ren, Guangfei Wang, Dejie Guo, Chao Lu, Yan Ma

    • Sugar addition caused vigorous proliferation of wilt pathogen.

    • Sugar addition modified bacterial community structure and decreased the diversity.

    • Sugar addition caused more complex and connected networks.

    • Keystone taxa formed positive links with wilt pathogen in sugar-spiked networks.

    Sugars are frequently and abundantly found in root exudates, but influence of specific sugars on the fate of soil-borne pathogens, microbiome structure, and particularly microbial interactions are not well understood. A 42-day of microcosm incubation was conducted with two soils: a natural watermelon Fusarium wilt pathogen (i.e., Fusarium oxysporum f. sp. niveum (FON))-infested soil (Low-FON soil) and the soil further receiving the wilt pathogen inocula (High-FON soil). Both soils were supplemented with four simple sugars before incubation. The results show that, in both soils, FON was enriched by all sugars although co-living with tremendously diverse microbes; and bacterial richness, evenness, and diversity were decreased and bacterial community structure was changed by all sugars. Bacterial richness and evenness were negatively correlated with FON quantity in both Low-FON and High-FON soils, indicating that FON may tend to live in soil with low alpha-diversity. In both Low-FON and High-FON soils, the sugar-spiked networks had more links, higher density, larger modules, and shorter harmonic geodesic distance, suggesting greater potentials for microbial interaction and niche-sharing. The positive links between some of the keystone taxa and FON indicates that these keystone taxa may have promoted FON. This may be one of reasons why FON could proliferate vigorously after sugar supplementation.

    Yitian Yu, Qi Zhang, Zhenyan Zhang, Nuohan Xu, Yan Li, Mingkang Jin, Guoqiang Feng, Haifeng Qian, Tao Lu

    • Continuous chlorine treatment have no obvious effect on soil microbial community structure and composition.

    • Residual chlorine slightly affected soil microbial functions.

    • Daily use of chlorine-containing disinfectants slightly threatened the soil ecosystem.

    Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application of chlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.

    Qi Zhang, Jing Ma, Alejandro Gonzalez-Ollauri, Yongjun Yang, Fu Chen

    ● Vegetation restoration of monoculture is not satisfactory in mining land.

    ● Native plants accelerated vegetation restoration and soil nutrient accumulation.

    ● Microbial enzymes boosted the initially slow nutritional metabolism of plantations.

    ● Soil microbial enzymes promoted positive succession of ecosystems.

    The diversity of vegetation configuration is the key to ecological restoration in open-pit coal mine dump. However, the recovery outcomes of different areas with the same vegetation assemblage pattern are completely different after long-term evolution. Therefore, understanding the causes of differential vegetation recovery and the mechanism of plant succession is of great significance to the ecological restoration of mines. Three Pinus tabulaeformis plantations with similar initial site conditions and restoration measures but with different secondary succession processes were selected from the open-pit coal mine dump that has been restored for 30 years. Soil physicochemical properties, enzyme activities, vegetation and microbial features were investigated, while the structural equation models were established to explore the interactions between plants, soil and microbes. The results showed that original vegetation configuration and soil nutrient conditions were altered due to secondary succession. With the advancement of the secondary succession process, the coverage of plants increased from 34.8% to 95.5% (P < 0.05), soil organic matter increased from 9.30 g kg −1 to 21.13 g kg−1 (P < 0.05), and total nitrogen increased from 0.38 g kg −1 to 1.01 g kg−1 (P < 0.05). The activities of soil urease and β-glucosidase were increased by 1.7-fold and 53.26%, respectively. Besides, the secondary succession also changed the soil microbial community structure and function. The relative abundance of Nitrospira genus which dominates the nitrification increased 5.2-fold. The results showed that urease and β-glucosidase promoted the increase of vegetation diversity and biomass by promoting the accumulation of soil organic matter and nitrate nitrogen, which promoted the ecological restoration of mine dumps.

    Qirui An, Yunyang Li, Na Zheng, Jincai Ma, Shengnan Hou, Siyu Sun, Sujing Wang, Pengyang Li, Xiaoqian Li, Chunmei Zhao

    • The relative abundance of rhizosphere soil bacteria has significantly positive correlation with BCF of Cd and Cu.

    • Obvious variations of predominant species of bacterial communities in rhizosphere soil would emerge in the additions with different concentrations of Cd-Cu mixtures.

    • In the additions with Cd and Cu, the mean of rhizosphere soil bacterial community diversity index was ranked as: Cu alone>Cd-Cu mixtures>Cd pollution.

    • The PCA and PERMANOVA analysis showed that Cu may be the main factor changing the composition of rhizosphere soil bacteria.

    To study the effects of combined Cd and Cu pollution on rhizosphere bacterial community. High-throughput sequencing was used to examine the response of rhizosphere bacterial communities to heavy-metal stress under single and mixed pollution of cadmium (Cd) and copper (Cu). With additions of Cd and Cu, the mean diversity index of rhizosphere bacterial community was in the order Cu alone>Cd-Cu mixtures>Cd alone. In all Cd and Cu treatments, the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. In the additions with different concentrations of Cd-Cu mixtures, LEfSe indicated that there were differences in the predominant species of rhizosphere bacterial communities. Some genera such as Streptomyces and Microbacterium belonging to Actinobacteria as biomarkers were significantly enriched in both control and treatments, while some genera such as Pseudoxanthomonas and Rhodopseudomonas belonging to Proteobacteria as biomarkers were observed to be enriched in the additions with single and mixture of Cd and Cu. According to the Nonmetric multidimensional scaling (NMDS) analysis, the structure of rhizosphere bacterial community was different between treatments and the CK. Principal Component Analysis (PCA) and permutational multivariate analysis of variance (PERMANOVA) showed that there were significant differences among treatments (p<0.01), and that the addition of Cu might be the primary factor affecting the composition of rhizosphere bacterial communities.

    Baile Xu, Gaowen Yang, Anika Lehmann, Sebastian Riedel, Matthias C. Rillig

    ● PFAS significantly increased litter decomposition and soil pH.

    ● Soil respiration was significantly inhibited by PFAS.

    ● Perfluorooctanesulfonic acid suppressed soil water-stable aggregates.

    ● Three PFAS exerted varying degrees of impact on soil health.

    Soils are impacted globally by several anthropogenic factors, including chemical pollutants. Among those, perfluoroalkyl and polyfluoroalkyl substances (PFAS) are of concern due to their high environmental persistence, and as they might affect soil structure and function. However, data on impacts of PFAS on soil structure and microbially-driven processes are currently lacking. This study explored the effects of perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA) and perfluorobutanesulfonic acid (PFBS) at environmental-relevant concentrations on soil health, using a 6-week microcosm experiment. PFAS (even at 0.5 ng g–1 for PFBS) significantly increased litter decomposition, associated with positive effects on β-glucosidase activities. This effect increased with PFAS concentrations. Soil pH was significantly increased, likely as a direct consequence of increased litter decomposition affected by PFAS. Soil respiration was significantly inhibited by PFAS in week 3, while this effect was more variable in week 6. Water-stable aggregates were negatively affected by PFOS, possibly related to microbial shifts. PFAS affected soil bacterial and fungal abundance, but not microbial and certain enzyme activities. Our work highlights the potential effects of PFAS on soil health, and we argue that this substance class could be a factor of environmental change of potentially broad relevance in terrestrial ecosystem functioning.

    Xin Sun, Mingjie Sun, Ying Chao, Xiaoyang Shang, Hui Wang, Hong Pan, Quangang Yang, Yanhong Lou, Yuping Zhuge

    ● Pb pollution significantly affected the diversity of microbial community structure.

    ● Pb pollution reduced the soil microbial biomass-carbon and nitrogen.

    ● Pb pollution increased invertase but reduced catalase activity.

    Lead (Pb) pollution is one of the most widespread and harmful environmental problems worldwide. Determination of changes in soil properties and microbial functional diversity due to land use is needed to establish a basis for remediation of soil pollution. This study aimed to investigate soils contaminated by Pb from different sources and to analyze the functional diversity and metabolism of soil microbial communities using Biolog technology. Pb pollution (> 300 mg kg−1) significantly influenced the diversity and metabolic functions of soil microbial communities. Specifically, Pb contamination significantly reduced soil microbial biomass carbon (C) and nitrogen (N) levels and catalase activity while increasing invertase activity. Furthermore, Biolog EcoPlate assays revealed that Pb pollution reduced the general activities of soil microorganisms, suppressing their ability to utilize C sources. In Pb-contaminated areas lacking vegetation cover, Shannon, Simpson, and McIntosh diversity indices of soil microorganisms were significantly reduced. The microbial diversity and biomass C and N levels were affected by land use and soil properties, respectively, whereas soil enzyme activity was primarily affected by the interaction between land use and soil properties. Our results provide a reference and a theoretical basis for developing soil quality evaluation and remediation strategies.

    Yumei Mao, Xiaoping Li, Warren A. Dick, Linkui Cao

    ● Gypsum can effectively decrease dissolved P loss via runoff and leachate from the areas with high soil P levels by increasing P uptake by ryegrass.

    ● Both surface application and mixing of gypsum into the topsoil reduced dissolved P losses.

    ● The effect of gypsum application method on dissolved P losses varied by soil texture.

    ● Flue gas desulfurization gypsum did not affect ryegrass biomass and also didn’t increase the accumulation of trace elements in soil and ryegrass.

    Controlling dissolved phosphorus (DP) loss from high P soil to avoid water eutrophication is a worldwide high priority. A greenhouse study was conducted in which flue gas desulfurization gypsum (FGDG) was applied by using different application methods and rates to two agricultural soils. Phosphorus fertilizer was incorporated into the soils at 2.95 g kg–1 to simulate soil with high P levels. The FGDG was then applied at amounts of 0, 1.5, and 15 g kg–1 soil on either the soil surface or mixed throughout the soil samples to simulate no-tillage and tillage, respectively. Ryegrass was planted after treatment application. The study showed that FGDG reduced runoff DP loss by 33% and leachate DP loss 38% in silt loam soil, and runoff DP loss 46% and leachate DP loss 14% in clay loam soil, at the treatment of 15 g kg–1 FGDG. Mixing applied method (tillage) provided strong interaction with higher FGDG. To overall effect, the mixing-applied method performed better in controlling DP loss from silt loam soil, while surface-applied (no tillage) showed its advantage in controlling DP loss from clay loam soil. In practice it is necessary to optimize FGDG concentrations, application methods, and DP sources (runoff or leachate) to get maximized benefits of FGDG application. The FGDG application had no negative effects on the soil and ryegrass.

    Stavros D. Veresoglou, Junjiang Chen, Xuheng Du, Qi Fu, QingLiu Geng, Chenyan Huang, Xilin Huang, Nan Hu, Yiming Hun, Guolin C. Li, Zhiman Lin, Zhiyu Ma, Yuyi Ou, Shuo Qi, Haitian Qin, Yingbo Qiu, Xibin Sun, Ye Tao, YiLing Tian, Jie Wang, Lingxiao Wu, Ziwei Wu, Siqi Xie, Ao Yang, Dan Yang, Chen Zeng, Ying Zeng, RuJie Zhang

    ● On average conventional tillage outperformed no tillage.

    ● Across fertilized trials, however, no tillage performed best.

    ● Aridity increases yield benefits of no tillage over conventional tillage.

    ● Fertile settings favor conventional tillage over no tillage.

    Reduced tillage practices present a tool that could sustainably intensify agriculture. The existing literature, however, lacks a consensus on how and when reduced tillage practices should get implemented. We reanalyzed here an extensive dataset comparing how regular tillage practices (i.e., conventional tillage) impacted yield of eight crops compared to stopping tillage altogether (i.e., no-tillage practice). We observed that aridity and fertilization favored no tillage over conventional tillage whereas conventional tillage performed better under high fertility settings. We further show that the responses are consistent across the crops. Our reanalysis complements the original and fills a gap in the literature questioning the conditions under which reducing tillage presents a viable alternative to common tillage practices.

    Yixin Sun, Xiaofang Du, Yingbin Li, Xu Han, Shuai Fang, Stefan Geisen, Qi Li

    ● Different primers will affect nematode annotation at different taxonomic levels.

    ● Sequencing analysis with different primers cannot be compared directly.

    ● 3NDf primers with NT database could provide more taxa than other combinations.

    High-throughput sequencing technology is increasingly used in the study of nematode biodiversity. However, the annotation difference of commonly used primers and reference databases on nematode community is still unclear. We compared two pairs of primers (3NDf/C_1132rmod, NF1F/18Sr2bR) and three databases (NT_v20200604, SILVA138/18s Eukaryota and PR2_v4.5 databases) on the determination of nematode community from four different vegetation types in Changbai Mountain, including mixed broadleaf-conifer forest, dark coniferous forest, betula ermanii Cham and alpine tundra. Our results showed that the selection of different primers and databases influenced the annotation of nematode taxa, but the diversity of nematode community showed consistent pattern among different vegetation types. Our findings emphasize that it is necessary to select appropriate primer and database according to the target taxonomic level. The difference in primers will affect the result of nematode taxa at different classification levels, so sequencing analysis cannot be used for comparison with studies using different primers. In terms of annotation effect in this study, 3NDf/C_1132rmod primers with NT_v20200604 database could provide more information than other combinations at the genus or species levels.

    Xinli Niu, Yongfan Cheng, Xiaopei Feng, Feng Sun, Yanfang Gu

    • Fertilizer increased soil nematode abundance and decreased the ecological index of soil nematode community.

    • Except for bacterivore density, weed species richness had no effect on soil nematode abundance and increased the ecological index of soil nematode community.

    • Fertilizer degraded, whereas weed species richness enhanced soil nematode community structure. Weed species richness may relieve the negative effect of fertilizer on the diversity of nematode community.

    Both fertilizer and plant species richness may affect the soil nematode community. However, the influence of fertilizer and weed species richness interaction is unclear. Nematode abundance and biodiversity in wheat and weed plots soil treated with nitrogen, phosphate and potassium fertilizer addition and weed species richness (0, 1, 2 and 4 weed levels) were investigated in a long-term microcosm experiment established in 2010 at Kaifeng, China. The results demonstrated that fertilizer treatment increased the abundance of total nematode, bacterivores, and plant parasites whereas it decreased the total genera number, the Shannon–Wiener diversity index (H′), Margalef richness index (SR), the total maturity index (∑MI), and structure index (SI), and degraded the structure of the nematode community. In contrast, weed species richness increased these ecological indices and enhanced the structure of the nematode community. Principal component analysis (PCA) indicated that the fertilizer's effect was more significant than weed species richness. Redundancy analysis demonstrated that fertilizer affected soil nematode mainly through increasing soil available phosphorus by 4.71 times and ammonium nitrogen content by 74.03%; weed species richness increased the diversity indices of soil nematode mainly through enhancing soil moisture by 2.07%. Our results suggest weed species richness may relieve the negative effect of fertilizer on the diversity of soil nematode community.

    Myo Thant, Xiaobing Lin, Anjana J. Atapattu, Min Cao, Shang-wen Xia, Shengjie Liu, Xiaodong Yang

    ● Strong associations among soil-wood feeders and fungus growers were observed.

    ● Weak associations between litter feeders and other feeders were observed.

    ● TPI and pH had effects on all feeding groups of termites.

    ● Plant biomass influenced soil-wood feeders and wood feeders.

    ● Litter mass influenced fungus growers, litter feeders, and soil feeders.

    The community composition and activity-density of termites can influence nutrient cycling and other ecological functions. However, the spatial distribution and the activity-density of termites on a fine-scale in tropical forests are still unknown. We checked the spatial distribution patterns of the feeding groups and species of termites and their co-occurrence pattern in a 1-ha (100 m × 100 m) plot, and their correlation with the environmental factors. We used a standard protocol to collect termite assemblages and classified them into five feeding groups based on their preferred diet: fungus growers, litter feeders, soil feeders, soil-wood feeders, and wood feeders. We measured the environmental factors: soil pH, litter mass, aboveground plant biomass, and topographic position index (TPI). Soil-wood feeders showed the highest activity-density, followed by wood feeders, fungus growers, soil feeders, and litter feeders. Soil-wood feeders and fungus growers demonstated a strong correlation while litter feeders showed weak correlations with other feeding groups. Termite feeding groups and most of the termite species displayed a positive association with the high TPI and the low soil pH patches. Our results indicated that the examined environmental factors influenced the termite community assemblages and distribution patterns on a fine-scale in tropical rainforests.

    Yali Wang, Yinsheng Li, Hongpei Geng, Qian Zuo, Michelle Thunders, Jiangping Qiu

    Ÿ 24 differentially expressed proteins (DEPs) were identified by proteomic method.

    Ÿ DEPs function as metabolism, signal transduction, stress-related and transport etc.

    Ÿ Proteomics of As exposure help to explore its toxicity mechanism in earthworm.

    Arsenic (As) is broadly distributed due to natural and anthropogenic sources, and it is toxic to organisms. This study aimed to investigate the proteomic response in earthworm exposed to As3+ . Earthworms were exposed to As3+ in soil at 5–80 mg kg–1, and samples were collected after 60 days exposure. Two-dimensional electrophoresis (2-DE) was used to separate the proteins in earthworm homogenate, then differentially expressed proteins (DEPs) were identified using MALDI-TOF/TOF-MS analysis. After 2-DE, 36 DEPs were found and 24 of them were successfully identified. 79.2% of DEPs were upregulated compared to the control group. The maximum fold change reached 53.8 in spot 3108 in the 80 mg kg–1 As group. Two proteins were not found in the control group but found in the As treated groups. Proteins were grouped into metabolism, signal transduction, stress-related, transport, regulation, and predicted/hypothetical protein categories based on their function. The protein–protein interaction between the DEPs indicated that serum albumin (ALB) is very important, related to 6 other proteins. Proteins were then verified by western blot, the results were in agreement with the proteomic analyses. The identification of induced or repressed proteins because of As3+ in earthworms is helpful to explore the underlying mechanisms of soil arsenic ecotoxicity.