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Soil Biology & Biochemistry
Pergamon Press.
Soil Biology & Biochemistry

Pergamon Press.

0038-0717

Soil Biology & Biochemistry/Journal Soil Biology & BiochemistrySCIISTPAHCI
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    Mutualistic interaction between arbuscular mycorrhiza fungi and soybean roots enhances drought resistant through regulating glucose exudation and rhizosphere expansion

    Hoang, Duyen Thi ThuRashtbari, MehdiAnh, Luu TheWang, Shang...
    10页
    查看更多>>摘要：Glucose is one of the low molecular weight components of root exudates to mediate the cross-talk between plants and microbes, but less is known about their contribution to drought resistance of plants and root-associated microbiome. To fill this knowledge gap, we optimized the visualization of glucose exudation and coupled it with another in situ tool - soil zymography -as well as destructive analysis of enzyme kinetics (beta-glucosidase; acid phosphomonoesterase) and microbial biomass. This helped identify how microbial functionality -affected by drought and P limitation -will show more resistance in the hotspots of soybean rhizosphere (grown in the rhizoboxes for 10 weeks) associated with arbuscular mycorrhizal fungi (AMF) symbiosis than those without AMF. Drought reduced glucose exudation, mainly allocated to root tips, and narrowed the rhizosphere enzymatic hotspot by three times. However, AMF inoculation enhanced glucose exudation compared to non-mycorrhizal plants and enlarged enzymatic hotspot area by 53% under drought condition. Despite the 50% reduction in beta-glucosidase and acid phosphomonoesterase activities owing to water deficit, AMF symbiont triggered up to 36% enzyme activities in correlation with the non-mycorrhizal ones. Therefore, the drought resistance of these two enzymes was enhanced by up to 63% in mycorrhizal plants. The biomass of microbial phosphorus increased by 45% under drought AMF-conditioned plants. We conclude that the cooperation between soybean and AMF induced the formation of favorable microsites around the root, specifically in overlapping localities between rhizosphere and mycorrhizosphere, characterized by enhanced glucose release, increasing rhizosphere expansion, high enzyme activities and shortened substrate turnover time. This, in turn, contributed to the stronger resistance of microbial functions (e.g., enzyme expression) to drought stress in the rhizosphere hotspots. Thus, in response to AMF inoculation and consequent high glucose availability, rhizosphere microorganisms increased P mining rate in those hotspots remaining active despite water scarcity.
      原文链接:
    • NSTL
    • Elsevier

    Nitrogen addition altered the plant-arbuscular mycorrhizal fungi network through reducing redundant interactions in an alpine meadow

    Lu, YawenLiu, XiangZhou, Shurong
    11页
    查看更多>>摘要：Interactions between plants and arbuscular mycorrhizal fungi (AMF) are pivotal in linking belowground soil nutrients with plant-derived carbon in terrestrial ecosystems. However, little is known about the effect of variation in soil nutrients (i.e., nitrogen enrichment) on the structure and phylogenetic characteristics of the mutualistic network. With a 7-year nitrogen addition experiment in an alpine meadow, we built networks for 20 plant species that all occur along the nitrogen addition gradient and their AMF by sequencing 314 root samples. We investigated the responses of association degree (i.e., the number of links of plant or AMF species), network connectance, nestedness, modularity and specialization to different concentrations of nitrogen addition. Phylogenetic signal was calculated to evaluate if the phylogenetically closely related plant species or AMF taxa share similar symbiosis partners. We found that nitrogen addition significantly reduced the plant and AMF association degree, with the generalist (with high association degree) and abundant AMF taxa in nature significantly decreasing association degree and relative abundance (sequencing reads). Therefore, the network connectance and nestedness decreased, but modularity increased with nitrogen addition. Phylogenetic signal of plants (i.e., phylogenetically related plants had similar AMF partners) was always stronger than that of AMF, but the signal vanished with nitrogen addition. The shifted soil properties after nitrogen addition, especially pH, played an important role in regulating the network structures. Our results discover a non-random plant-AMF network shaped by both phylogeny and soil environments in an alpine meadow, and suggest that global nitrogen addition may result in a non-random loss or switch of plant-fungal associations, changes in network structures and phylogenetic relationships, which may have ramification to nutrient exchange and symbiotic performance.
      原文链接:
    • NSTL
    • Elsevier

    Aggravation of nitrous oxide emissions driven by burrowing crab activities in intertidal marsh soils: Mechanisms and environmental implications

    An, ZhiruiZheng, YanlingHou, LijunGao, Dengzhou...
    10页
    查看更多>>摘要：Coastal wetlands are hotspots for nitrogen (N) cycling and a significant natural source of the potent greenhouse gas nitrous oxide (N2O). Burrowing benthos are known to transform N in intertidal marsh soils, but their contribution to N2O emissions and the underlying molecular mechanisms remain unclear. Here, the effects of crab bioturbation on N2O emissions in coastal marshes, where Chiromantes dehaani and Helice tridens tientsinensis were the dominant crab species, were investigated in field and indoor experiments. The N2O emissions increased significantly in the presence of crabs, being positively correlated with the intensity of crab bioturbation but differing among crab species. Natural-abundance isotope analyses indicated that crab bioturbation greatly promoted the contribution of hydroxylamine oxidation to N2O production; nevertheless, bacterial denitrification (including heterotrophic denitrification and nitrifier denitrification) remained the dominant pathway. Molecular analyses suggested that the increased N2O emissions in crab-disturbed habitats might be driven by underlying changes to microbial communities, especially by the disproportionate stimulation of nitric oxide reductase-carrying microbes over nitrous oxide reductase-carrying microbes. This study highlights the importance of considering the burrowing activity, density, and species of benthos when evaluating the N cycle in coastal wetlands.
      原文链接:
    • NSTL
    • Elsevier

    Carbon cycle in the microbial ecosystems of biological soil crusts

    Wang, QiongZhang, QingyiHan, YingchunZhang, Delu...
    12页
    查看更多>>摘要：The carbon cycle (C-cycle) is the most important and complex biogeochemical cycle in soil ecosystems, but our understanding of C-cycle at the community level remains limited. Biocrusts are known ecosystem engineers and represent ideal model systems for biogeochemical cycling studies. Here, metagenomic sequencing based on five repeated collections of four types of biocrusts revealed a low abundance of genes related to light-driven inorganic carbon fixation, and high abundance of genes related to the chemical energy-driven degradation of macromolecular organic carbon (OC), fermentation, aerobic respiration, and CO oxidation. For OC decomposition, genes mediating starch/glycogen and cellulose degradation were most abundant during the initial complex OC degradation, as were genes mediating fermentation during terminal steps of OC decomposition. To assess successional changes in carbon cycle, the metagenomic data were combined with absolute quantification via GeoChip, as well as key enzyme activity measurements. Inorganic carbon fixation, fermentation, CH4 oxidation, and both starch/glycogen and peptidoglycan degradation decreased during succession. However, several high efficiency processes, as well as CO oxidation and most types of OC degradation, increased. Co-occurrence networks revealed that C-cycle in biocrusts consists of an assimilation module, akin to primary production, and a dissimilation module, comparable to secondary production; dynamic changes in the relationships between C cycle pathways and microbial community composition occurred during succession. The two C-cycle modules were connected by the Calvin-Benson-Bassham cycle, as well as ethanol and propionate fermentation; the modules were balanced by drought and salinity. Collectively, these results improve our understanding of C-cycle pathways and regulatory mechanisms in biocrust succession, and provide a basis for future multi-omics studies of these systems.
      原文链接:
    • NSTL
    • Elsevier

    Specific utilization of biopolymers of plant and fungal origin reveals the existence of substrate-specific guilds for bacteria in temperate forest soils

    Algora, CameliaOdriozola, InakiHuman, Zander RainierHoll, Sandra Awokunle...
    10页
    查看更多>>摘要：Bacteria play critical roles in soil ecosystems when decomposing structural components of biomass. However, the ability of individual bacterial taxa to utilize various biopolymers is understudied, hampering our understanding of the role of bacteria in the soil carbon cycle. Here, we in situ incubated in forest litter various biopolymers of plant and fungal origin - cellulose, xylan, glucomannan, pectin, lignin, 0-1,3-glucan, 0-1,3-1,6-glucan, and chitin - to identify bacteria that associated with them during decomposition. After an incubation time of three weeks, all biopolymers were colonized by substantial bacterial numbers. The bacterial communities established on each biopolymer were specific, differing from the community on the surrounding plant litter, which indicates specialization in biopolymer utilization and the existence of distinct substrate-specific guilds. Members of Proteobacteria and Bacteroidetes predominated in all guilds. However, several biopolymers hosted members of other phyla: bacteria affiliated with Planctomycetes were enriched on cellulose, Acidobacteria on xylan, Actinobacteria on pectin, and Firmicutes on glucomannan and 0-1,3-1,6-glucan. The communities on lignin had low diversity, were phylogenetically clustered and were mainly composed of Proteobacteria. The communities on chitin showed higher diversity than those on other biopolymers. Approximately 80% of biopolymer-associated bacteria were specialists and were recovered from only one or two biopolymers. Only three specific phylotypes affiliated with Burkholderia, Klebsiella and Hafnia were present on all biopolymers. Bacterial isolation confirmed the involvement of Bacteroidetes in the decomposition of chitin, Firmicutes in the decomposition of glucomannan and 0-glucans, and the abundance of decomposers from Proteobacteria on all biopolymers. The proliferation of bacteria was observed on all fungally derived biopolymers and most plant-derived biopolymers. Exceptions were pectin and xylan, where bacterial counts were low - three orders of magnitude lower than in the surrounding plant litter. The results indicate the involvement of distinct, substrate-specific guilds of bacteria in the utilization of biopolymers in forest topsoil. Furthermore, by classifying soil bacteria into substrate-specific guilds, this paper contributes to efforts to assign functional traits of ecological relevance to individual members of the microbial community.
      原文链接:
    • NSTL
    • Elsevier

    Earthworm invasion shifts trophic niches of ground-dwelling invertebrates in a North American forest

    Ferlian, OlgaCesarz, SimoneLochner, AlfredPotapov, Anton...
    10页
    查看更多>>摘要：Earthworms are invading soil communities worldwide, and their actions as decomposers and ecosystem engineers are vastly impacting many ecosystem functions. In the northern regions of North America, invasive earthworms are often functionally distinct from the native invertebrate fauna and, thus, typically occupy empty trophic niches in soil food webs. Nevertheless, they can affect the co-occurring soil invertebrate communities in multiple indirect ways. Particularly, the redistribution and removal of litter resources can affect feeding interactions of soil biota that channel up to higher trophic levels, such as predators, causing shifts across all components of the soil food web, which are hard to investigate. To study trophic shifts in earthworm-invaded soil communities, we used ground predators as model organisms since they occupy high trophic levels and connect different energy channels in soil food webs. We used stable isotope (13C and 15N) and fatty acid analyses as complementary tools to describe the trophic levels and basal resources of consumers that were impacted by earthworm invasion, specifically examining the trophic niches and resources available to ground-dwelling invertebrates of a northern aspen forest. The distinct trophic niches of invertebrate species were affected significantly by earthworm invasion. Shifts in neutral lipid fatty acid profiles as well as decreases in animal Delta 13C and Delta 15N signatures indicated changes in basal resources and trophic levels, respectively. Furthermore, we observed a trend of greater intra-specific and less inter-specific variation in fatty acid profiles of soil organisms following earthworm invasion. Notably, shifts in marker fatty acids of ground-dwelling invertebrates were opposite to the changes observed in soil microbial communities, suggesting de-coupling of soil microbial and ground arthropod food-web compartments. Overall, our study revealed a systemic effect of invasive earthworms on grounddwelling invertebrates. Earthworms presumably consumed a considerable amount of resources, such as litter and, thus, incorporated them in the soil food web, which was, as a basal resource, not available in the food web free of earthworms. Overall, the ground-dwelling invertebrates have adapted (changed their trophic function) which could explain the balancing of potential environmental changes that are caused by invasive earthworms. This observation potentially explains why these species are dominant in the studied forest and resist earthworm invasion. Future studies should investigate if altered litter availability also causes shifts in soil biodiversity in invaded forests, which is assumed but rarely directly tested to date.
      原文链接:
    • NSTL
    • Elsevier

    Arbuscular mycorrhizal fungi have a greater role than root hairs of maize for priming the rhizosphere microbial community and enhancing rhizosphere organic P mineralization

    Zhou, JiachaoZhang, LinFeng, GuGeorge, Timothy S....
    12页
    查看更多>>摘要：Root hairs, arbuscular mycorrhizal (AM) fungi and rhizosphere microbiome all play important roles in mycorrhizal plant phosphorus (P) absorption. However, how the plant-AM fungi-rhizosphere microbiome continuum interacts efficiently to promote the use of soil P is still unclear. Here, we present results of a controlled environment experiment to reveal the effect of root hair, AM fungi and their interaction on rhizosphere microbial Po cycles. Compared to root hairs, AM fungi contributed more to active microbial community assembly, functional gene recruitment and Po mineralization. The rhizosphere microbial Po mineralizing process contributed more than half of plant P assimilation in the P limited condition. The application of inorganic P (Pi) reduced the effect of root hairs and AM fungi on rhizosphere microbial community assembly and Po mineralizing ability. Our findings demonstrate the importance of AM fungi for maize as a driving force for rhizosphere microbial recruitment and function.
      原文链接:
    • NSTL
    • Elsevier

    Comammox Nitrospira play a minor role in N2O emissions from an alkaline arable soil

    Jiang, YishunLiang, YongchaoTan, CheYin, Chang...
    11页
    查看更多>>摘要：Nitrogen addition to croplands greatly increases global emissions of the potent greenhouse gas nitrous oxide (N2O). Three ammonia-oxidizing functional guilds constitute the major producers of N2O in agricultural soils, but their relative contributions are still poorly understood, especially the newly discovered and widespread complete ammonia oxidizers (comammox). To fill this knowledge gap, we used three nitrification inhibitors: acetylene, 1octyne, and 3,4-dimethylpyrazole phosphate (DMPP), to selectively suppress the activity of different ammonia oxidizer guilds to discriminate their relative contributions to N2O production in an alkaline arable soil. The results indicated that DMPP completely inhibited the growth of comammox Nitrospira clade A and ammonia oxidizing bacteria (AOB) but promoted ammonia-oxidizing archaea (AOA) growth, while the abundance of comammox Nitrospira clade A increased in the presence of 1-octyne at high ammonium (NH4+) concentrations. AOB dominated N2O production in soils with inorganic NH4+ amendment, followed by AOA, while comammox Nitrospira contributed to less than 3% of total N2O emissions with an N2O yield of ~0.083% (N2O per molecule of nitrate). The abundance of comammox Nitrospira clade A was approximately two orders of magnitude lower than that of canonical ammonia-oxidizers. Phylogenetic analysis revealed that the majority of comammox Nitrospira clade A belonged to a new cluster that was separated from the known comammox bacterium. Taken together, our results clearly and strongly demonstrate that comammox Nitrospira play only a minor role in N2O emissions in a heavily fertilized alkaline arable soil.
      原文链接:
    • NSTL
    • Elsevier

    Microbial communities along the soil-root continuum are determined by root anatomical boundaries, soil properties, and root exudation

    Zhou, YiWei, YanliZhao, ZhongjuanLi, Jishun...
    11页
    查看更多>>摘要：The microbiome in plant-soil systems has a significant influence in promoting plant growth. Despite this, the extent of selectivity that the plant exerts on the microbiome in the continuum between the soil and internal plant tissues is not well understood. This study analysed the root microbiome of a legume, Melilotus officinalis (L.) Pall., sweet clover, and focused on dynamic shifts in the microbial community structure through the niches of bulk soil, rhizosphere, periderm, phloem and xylem, and further examined the effects of soil factors, root exudate metabolism, and root cell wall development on microbiome assemblages in different root compartments. Young and mature plants were sampled at 24 field sites and the microbial communities in different niches from bulk soil and rhizosphere through to root compartments were analysed by 16S rRNA gene sequencing. The microbiome composition changed from periderm to phloem to a greater extent than across other boundaries. Variation in microbiome composition was associated with geographic distance and soil properties for the bulk soil, rhizosphere and periderm niches. Root exudation influenced the rhizosphere microbiome assemblages in young and mature plants. The endophyte communities that occupied the phloem and xylem were most conserved and were independent of growing environments and root exudation. Symbiotic rhizobia able to nodulate M. officinalis were prominent colonisers of the periderm (~15%) and xylem (~6.2%), but were only a minor component in other soil-related niches (0.1%-2.5%). In xylem tissues, endophyte diversity was correlated with the total cell wall and lignin content across the sampled sites (r = 0.29-0.62). Our results demonstrate that selection of microbiome constituents occurs at different boundaries through bulk soil, rhizosphere, periderm, phloem and xylem, and is especially strong across the periderm boundary. The conserved endophyte community in the innermost tissues (phloem and xylem) was identified, and will be potentially advantageous to the development of specific beneficial microbial inoculants.
      原文链接:
    • NSTL
    • Elsevier

    Invasive earthworms alter forest soil microbiomes and nitrogen cycling

    Jang, JeonghwanXiong, XianyiLiu, ChangYoo, Kyungsoo...
    11页
    查看更多>>摘要：Northern hardwood forests in formerly glaciated areas had been free of earthworms until exotic European earthworms were introduced by human activities. The invasion of exotic earthworms is known to dramatically alter soil physical, geochemical, and biological properties, but its impacts on soil microbiomes are still unclear. Here we show that the invasive earthworms alter soil microbiomes and ecosystem functioning, especially for nitrogen cycling. We collected soil samples at different depths from three sites across an active earthworm invasion chronosequence in a hardwood forest in Minnesota, USA. We analyzed the structures and the functional potentials of the soil microbiomes by using amplicon sequencing, high-throughput nitrogen cycle gene quantification (NiCE chip), and shotgun metagenomics. Both the levels of earthworm invasion and soil depth influenced the microbiome structures and the functional gene abundances. In the most recently and minimally invaded soils, Nitrososphaera and Nitrospira as well as the genes related to nitrification were more abundant than in the heavily invaded soils. By contrast, genes related to denitrification and nitrogen fixation were more abundant in the heavily invaded than the minimally invaded soils at various depths. Since denitrification can cause a nitrogen loss from the ecosystem, our results suggest the invasion of earthworms could influence the overall forest N cycling.
      原文链接:
    • NSTL
    • Elsevier