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Soil carbon (C) plays a critical role in the global C cycle and has a profound effect on climate change. To obtain an in-depth and comprehensive understanding of global soil C changes and better manage soil C, all meta-analysis results published during 2001–2019 relative to soil C were collected and synthesized. The effects of 33 influencing factors on soil C were analyzed, compared and classified into 5 grades according to their effects on soil C. The effects of different categories of influencing factors, including land use change (LUC), management and climate change, on soil C and the underlying mechanism were compared and discussed. We propose that natural ecosystems have the capacity to buffer soil C changes and that increasing C inputs is one of the best measures to sequester C. Furthermore, a comparison between the meta-analyses and previous studies related to soil C based on bibliometric analysis suggested that studies on wetland soil C, soil C budgets and the effects of pollution and pesticides on soil C should be strengthened in future research.

Little known the connections between soybeans mitogen-activated protein kinase (MAPK) gene expression and the rhizomicrobiome upon invasion of the root pathogen Fusarium oxysporum. To address this lack of knowledge, we assessed the rhizomicrobiome and root transcriptome sequencing of wild and cultivated soybean during the invasion of F. oxysporum. Results : indicated F. oxysporum infection enriched Bradyrhizobium spp. and Glomus spp. and induced the expression of more MAPKs in the wild soybean than cultivated soybean. MAPK gene expression was positively correlated with Pseudomonadaceae but negatively correlated with Sphingomonadaceae and Glomeraceae in both cultivated and wild soybean. Specifically, correlation profiles revealed that Pseudomonadaceae was especially correlated with the induced expression of GmMAKKK13-2 (Glyma.14G195300) and GmMAPK3-2 (Glyma.12G073000) in wild and cultivated soybean during F. oxysporum invasion. Main fungal group Glomeraceae was positively correlated with GmMAPKKK14-1 (Glyma.18G060900) and negatively correlated with GmRaf6-4 (Glyma.02G215300) in the wild soybean response to pathogen infection; while there were positive correlations between Hypocreaceae and GmMAPK3-2 (Glyma.12G073000) and between Glomeraceae and GmRaf49-3 (Glyma.06G055300) in the wild soybean response, these correlations were strongly negative in the response of cultivated soybean to F. oxysporum. Taken together, MAPKs correlated with different rhizomicrobiomes indicating the host plant modulated by the host self-immune systems in response to F. oxysporum.

Rice is a staple food for the world’s population. However, the straw produced by rice cultivation is not used sufficiently. Returning rice straw to the field is an effective way to help reduce labor and protect the soil. This study focused on the effect of water-covered depth with the freeze–thaw cycle on rice straw decomposition and the soil fungal community structure in a field in Northeast China. The field and controlled experiments were designed, and the fungal ITS1 region was tested by high-throughput sequencing for analyzing the fungal communities in this study. The results showed that water coverage with the freeze–thaw cycle promoted the decomposition of rice straw and influenced the fungal community structure, by analyzing the network of the fungal communities, it was found that the potential keystone taxa were Penicillium, Talaromyces, Fusarium, and Aspergillus in straw decomposition, and the strains with high beta-glucosidase, carboxymethyl cellulase, laccase, lignin peroxidase, and manganese peroxidase could also be isolated in the treated experiment. Furthermore, plant pathogenic fungi were found to decrease in the water-covered treatment. We hope that our results can help in rice production and straw return in practice.

Wild varieties of plants have stronger stress resistances than their cultivated relatives, and rhizosphere bacteria play an important role in improving the environmental adaptabilities of plants. However, the responses and adaptations of bacterial communities to wild soybean (Glycine soja Sieb. et Zucc) and cultivated soybean (Glycine max L.) have rarely been studied. Thus, the aim of this study was to investigate the differences in the rhizosphere bacterial communities of wild and cultivated soybeans under field and potted conditions using metagenomic analysis. The results showed that the rhizosphere bacterial diversity was higher in wild soybean than that in cultivated soybean in field samples, indicating that domestication leads to a decrease in the rhizosphere bacterial diversity of cultivated soybean. In addition, the higher RAs of beneficial and plant growth-promoting bacteria such as Acidobacteria, Gemmatimonadetes,Bradyrhizobium and Bacillus were in the wild soybean rhizosphere, illustrating that wild soybean has a stronger environmental resistance and adaptation than cultivated soybean. Meanwhile, soil pH, soil organic carbon, total nitrogen, total phosphorus, available phosphorus, and available potassium were significantly correlated with rhizosphere bacteria. Collectively, the rhizosphere bacteria of wild and cultivated soybean were different, wild soybeans increase the numbers of beneficial microbes in the rhizosphere to improve their environmental adaptability, and the utilization of wild resources might be an effective way to improve crop stress resistance.

Wetland cultivation has a profound effect on soil organic carbon (SOC) and global soil carbon cycles. However, the global patterns of the changes in SOC following wetland cultivation are still not well understood, especially with respect to the conditions under which SOC can increase in cultivated wetlands. We synthesized the results from 64 study sites and carried out a meta-analysis to quantify the changes in SOC following wetland cultivation and identify the underlying mechanisms. Although wetland cultivation led to a reduction in SOC under most conditions, wetland cultivation may result in an increase (p

Asian cultivated rice (Oryza sativa L.) domesticated from common wild rice (Oryza rufipogon Griff.) is one of the most consumed staple foods in the world. The rhizomicrobiome plays a vital role in the growth and production of rice. However, the responses of rhizomicrobial community structures to rice cultivation (including agricultural management and rice breeding) and natural environmental shifts are largely unknown. In this study, the rhizomicrobiomes of cultivated rice grown in paddy fields and wild rice grown in natural ecosystems were compared on a regional scale using high-throughput sequencing. For the same location, the cultivated rice showed less selective pressure on the rhizomicrobiome than wild rice. Specifically, compared to the rhizomicrobiome of wild rice, that of cultivated rice had 1) more complicated networks with stronger connections among different groups and 2) higher diversity, as evidenced by the Shannon, Simpson, ACE and Chao1 indices. For different locations, the rhizomicrobiome of cultivated rice was more sensitive to environmental shifts than that of wild rice. Compared to natural ecosystems, in paddy fields, 1) the rhizomicrobial diversity changed more drastically; 2) the number of rhizomicrobial groups cooccurring in different regions was lower at almost all taxonomic levels; and 3) the differences among samples examined by ANOSIM and PERMANOVA tests were more significant. In addition, we observed that the effects of rice cultivation on the rhizomicrobiome were more significant than those of natural environmental shifts on a large scale. Taken together, our results indicate that rice cultivation has profound effects on the rice rhizomicrobiome and that the rhizomicrobiome of cultivated rice in agricultural ecosystems is more sensitive to environmental shifts than that of wild rice in natural ecosystems.

Dongxiang common wild rice (CWR) is extremely cold tolerant, which can grow at the northernmost latitudes. To take full advantage of Dongxiang CWR���s cold tolerance for rice production and breeding, it is important to obtain a deep understanding of the mechanism underlying its cold tolerance. In this study, the rhizospheric microbiome of CWR was investigated and compared with that of Leersia hexandra Swartz (LHS) in Dongxiang to clarify the role of the rhizospheric microbiome in CWR cold tolerance. The results showed that, compared with the LHS rhizospheric microbiome, the CWR rhizospheric microbiome was less diverse and smaller, as indicated by its lower diversity and richness indices and fewer detected groups, core genera, and indicator genera. However, a larger proportion of the CWR indicator genera and unique genera, including Acidiphilium, Mortierella, Glomus, etc. showed the ability to adapt to low temperatures, indicating that CWR was more likely to be associated with microbial groups that may enhance cold tolerance. The results indicated that the extreme cold tolerance of Dongxiang CWR benefited from its rhizospheric microbiome, and this cold tolerance was speculated to benefit more from key microbial groups (indicator genera and unique genera) than from microbial diversity.

Additional file 1: Fig. S1. The numbers of published papers with meta-analyses related to soil carbon and all studies related to soil carbon from 2009 to 2018. Fig. S2. Keyword distributions of meta-analyses and all studies related to soil carbon. The bar plot indicates the percentage changes in keyword distributions in the 11 ecosystems, 12 indices and 29 influencing factors between the meta-analyses and all studies related to soil carbon. The network indicates the keyword distributions in the 11 ecosystems, 12 indices and 29 influencing factors and the co-occurrence frequency of two groups; the vertex indicates the relative percentage of each group; the numerical value of the vertex of each group = 50 * keyword count of each group/the maximum keyword count; and the edges indicate the co-occurrence frequency of two groups. The numerical value of the edge of each group = 50 * co-occurrence frequency of each pair of two groups/the maximum co-occurrence frequency. Table S1. Changes in C losses and C assimilation due to different influencing factors. The C losses include CO2 emissions, CH4 emissions and carbon decomposition. C assimilation includes underground biomass, aboveground biomass, plant biomass, net primary production and so on. NA means that no data were reported in the studies or that there were not enough data for the t-tests. Table S2. List of the references that the meta-analysis results were collected.

The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops.

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession.

To understand the impact of wetland cultivation and restoration on soil microbes and the corresponding soil biogeochemical processes, an experiment was established that included three cultivated treatments (marshes with 5, 15, and 25 years (CU05, CU15 and CU25) of soybean cultivation), two restored treatments (with 6 and 12 years (RE06 and RE12) of agricultural abandonment), and a natural marsh (NAT) as a reference. Changes in soil properties and microbial communities across the different treatments were analyzed. The results showed that soil microbial biomass and almost all the measured nutrients decreased in the order of NAT, restored treatments and cultivated treatments. Soil microbial structures in restored treatments were more similar to those of NAT than those of cultivated treatments. Specifically, the soil microbial communities of NAT and restored treatments were distinguished by a higher relative abundance of fungi, which were positively influenced by soil organic carbon and total nitrogen. In contrast, cultivated treatments were characterized by a higher relative abundance of gram-positive bacteria, which were positively influenced by the C/N ratio. The results indicated that the degraded soil in cultivated treatments began to recover after agricultural abandonment. However, the differences in soil microbial structures between restored treatment and NAT soils indicated that 12 years of restoration was not sufficient to restore the cultivated marshes to their natural status. Among all the measured soil properties, soil organic carbon and available potassium were identified as the main drivers of soil microbial communities, while the effect of pH on soil microbes was insignificant in this study. As available phosphorus was significantly decreased in the soil of restored treatments, phosphorus addition might be an effective way to accelerate the restoration process.

The community assembly change of arbuscular mycorrhizal fungi (AMF) during the reclamation of wetlands to paddy fields is mostly unknown. In this study, we applied the high-throughput sequencing te...

Oryza rufipogon is the ancestor of human-cultivated Oryza sativa. However, little is known about the difference between the root-associated microorganisms of O. rufipogon and O. sativa. In this study, the root-associated bacteria of O. rufipogon, Leersia hexandra, and O. sativa from different latitudes in China were studied by DGGE analysis. Their bacterial community structures were compared by principal component analysis. The relationship between root-associated bacteria and soil properties was explored by canonical correspondence analysis. The relationships of glomalin-related soil protein (GRSP) content, soluble sugar content, proline content of the plant, and bacterial diversity indices of their root-associated microorganisms were also investigated. We found both broad-spectrum and host-specific bacteria, and the similarity, diversity and abundance indices of O. rufipogon and L. hexandra were higher than O. sativa root-associated bacteria. However, even living in the same habitat, O. rufipogon and L. hexandra selected different root-associated bacteria. Microbial composition was primarily correlated with available N, P, and K and the annual precipitation. We also found a positive correlation between the soluble sugar content of the plant and GRSP content of the root soil. The above results indicated that the community structure of root-associated bacteria differs between wild rice and cultivated rice. Human activity and the natural selection of the host plants shaped the differences, consistent with our hypothesis.