High-Throughput Sequencing Reveals the Diversity and Community Structure in Rhizosphere Soils of Three Endangered Plants in Western Ordos, China.

China's western Ordos is a distribution area for the extremely precious remnants of ancient Asian environments, which in endangered plant species and complex ecosystems. Accordingly, in this study, we collect three endangered plants belonging to the Zygophyllaceae family, namely Tetraena mongolica, Sarcozygium xanthoxylon, and Nitraria tangutorum Bobr. High-throughput sequencing technology was applied to study microbial diversity in these plant rhizosphere soils. Analysis of species composition abundance, Alpha diversity, Beta diversity and microbial structure are analyzed. 2428 bacterial OTUs and 1256 fungal OTUs are obtained from the rhizosphere soils, and the bacterial and fungal sequencing coverage is above 99%. Bacilli are the most abundant (86.91%) in the bacterial community. The fungal community has significant differences in three plants. The abundances of the genus Dothideomycetes in the rhizosphere soils of Tetraena mongolica and Sarcozygium xanthoxylon plants are the highest, which are 44.57% and 37.69%, respectively. Thus, Dothideomycetes is the dominant bacteria in the community. The genus Sordariomycetes in the rhizosphere soil is the dominant fungi with a relative abundance of 41.04%. Redundancy analysis revealed that microbial communities were closely related to environmental factors. Overall, this study bring new insights into the relationship between rhizosphere soils microbial diversity and environment to improving the adaptability of the endangered plants in survival environment.

AM fungal diversity and its impact across three types of mid-temperate steppe in Inner Mongolia, China.

Arbuscular mycorrhizal (AM) fungal diversity was measured in three different natural mid-temperate steppe types: the meadow steppe, typical steppe, and desert steppe. In these steppe soils, 24 AM fungal species from eight genera were identified, in which Glomus had the highest relative abundance. Funneliformis geosporus, Glomus microaggregatum, and Septoglomus constrictum had high relative abundance and were found widely across varying soil depth and steppe type. Meadow steppes had significantly higher AM fungal species richness compared to typical steppes and desert steppes, but there was no significant difference between typical steppes and desert steppes. AM fungal spore density, two Bradford-reactive soil protein (BRSP) fractions, and extraradical hyphal length densities (HLDs) were significantly different among the three steppe types. Alkaline phosphatase and acid phosphatase activity, urease activity, and soil bacterial and actinomycotic quantity were significantly related to the AM fungal spore density and species richness in these arid and semi-arid steppes. Therefore, steppe types could influence the distribution pattern of AM fungal diversity and the content of glomalin-related soil protein (GRSP).

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas.

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

Effects of compost as a soil amendment on bacterial community diversity in saline-alkali soil.

Introduction: Soil salinization poses a worldwide challenge that hampers agricultural productivity. Methods: Employing high-throughput sequencing technology, we conducted an investigation to examine the impact of compost on the diversity of bacterial communities in saline soils. Our study focused on exploring the diversity of bacterial communities in the inter-root soil of plants following composting and the subsequent addition of compost to saline soils. Results: Compared to the initial composting stage, Alpha diversity results showed a greater diversity of bacteria during the rot stage. The germination index reaches 90% and the compost reaches maturity. The main bacterial genera in compost maturation stage are Flavobacterium, Saccharomonospora, Luteimonas and Streptomyces. Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla in the soil after the addition of compost. The application of compost has increased the abundance of Actinobacteria and Chloroflexi by 7.6 and 6.6%, respectively, but decreased the abundance of Firmicutes from 25.12 to 18.77%. Redundancy analysis revealed that soil factors pH, solid urease, organic matter, and total nitrogen were closely related to bacterial communities. Discussion: The addition of compost effectively reduced soil pH and increased soil enzyme activity and organic matter content. An analysis of this study provides theoretical support for compost's use as a saline soil amendment.

Microbial Assemblages Associated with the Soil-Root Continuum of an Endangered Plant, Helianthemum songaricum Schrenk.

The microbial network of the soil-root continuum plays a key role in plant growth. To date, limited information is available about the microbial assemblages in the rhizosphere and endosphere of endangered plants. We suspect that unknown microorganisms in roots and soil play an important role in the survival strategies of endangered plants. To address this research gap, we investigated the diversity and composition of the microbial communities of the soil-root continuum of the endangered shrub Helianthemum songaricum and observed that the microbial communities and structures of the rhizosphere and endosphere samples were distinguishable. The dominant rhizosphere bacteria were Actinobacteria (36.98%) and Acidobacteria (18.15%), whereas most endophytes were Alphaproteobacteria (23.17%) as well as Actinobacteria (29.94%). The relative abundance of rhizosphere bacteria was higher than that in endosphere samples. Fungal rhizosphere and endophyte samples had approximately equal abundances of the Sordariomycetes (23%), while the Pezizomycetes were more abundant in the soil (31.95%) than in the roots (5.70%). The phylogenetic relationships of the abundances of microbes in root and soil samples also showed that the most abundant bacterial and fungal reads tended to be dominant in either the soil or root samples but not both. Additionally, Pearson correlation heatmap analysis showed that the diversity and composition of soil bacteria and fungi were closely related to pH, total nitrogen, total phosphorus, and organic matter, of which pH and organic matter were the main drivers. These results clarify the different patterns of microbial communities of the soil-root continuum, in support of the better conservation and utilization of endangered desert plants in Inner Mongolia. IMPORTANCE Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment. Therefore, the profound study of the microbial diversity of rare desert plants can provide important data to support the protection and utilization of rare desert plants. Accordingly, in this study, high-throughput sequencing technology was applied to study the microbial diversity in plant roots and rhizosphere soils. We expect that research on the relationship between soil and root microbial diversity and the environment will improve the survival of endangered plants in this environment. In summary, this study is the first to study the microbial diversity and community structure of Helianthemum songaricum Schrenk and compare the diversity and composition of the root and soil microbiomes.

Soil microbial community composition and co-occurrence network responses to mild and severe disturbances in volcanic areas.

Soil physicochemical properties and vegetation types are the main factors affecting soil microorganisms, but there are few studies on the effects of the disturbance following volcanic eruption. To make up for this lack of knowledge, we used Illumina Miseq high-throughput sequencing to study the characteristics of soil microorganisms on both shores of a volcanically disturbed lake. Soil microorganisms in the two sites were subjected to different degrees of volcanic disturbance and showed significant heterogeneity. Mild volcanic disturbance area had higher enrichment of prokaryotic community. Co-occurrence network analysis showed that a total of 12 keystone taxa (9 prokaryotes and 3 fungi) were identified, suggesting that soil prokaryote may play a more significant role than fungi in overall community structure and function. Compared with severe volcanic disturbance area, the soil microbial community in mild volcanic disturbance area had the higher modular network (0.327 vs 0.291). The competition was stronger (positive/negative link ratio, P/N: 1.422 vs 1.159). Random forest analysis showed that soil superoxide dismutase was the most significant variable associated with soil microbial community. Structural equation model (SEM) results showed that keystone had a directly positive effect on prokaryotic (λ = 0.867, P < 0.001) and fungal (λ = 0.990, P < 0.001) multifunctionality while had also a directly positive effect on fungal diversity (λ = 0.553, P < 0.001), suggesting that keystone taxa played a key role in maintaining ecosystem stability. These results were important for understanding the effects of different levels of volcanic disturbance on soil ecosystems.

Patterns and drivers of microbiome in different rock surface soil under the volcanic extreme environment.

Soil microbial communities were investigated under the volcanic extreme environment. Soil bacterial networks exhibited higher stability than fungal networks. Holocene granite had a more complex microbial network than basalt. Soil pH and total protein were key drivers of microbial network stability.

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis.

Root-associated microbiomes play significant roles in plant productivity, health and ecological services. However, our current understanding of the microbial assemblages in the rhizosphere and endosphere of herbage is still limited. To gain insights into these microbial assemblages, Illumina MiSeq high-throughput sequencing was performed to investigate the characteristics of microbial communities of an herbage, Leymus chinensis. Hierarchical clustering analysis and principal coordinate analysis (PCoA) results showed that microbial communities of the rhizosphere and endosphere samples were clearly distinguished. Rhizosphere soil communities showed a greater sensitivity than root endosphere communities using linear discriminant analysis (LDA) effect size (LEfSe). Rhizosphere and endosphere communities performed their respective functions in the soil as a cohesive collective, and Rhizobiales were observed to function as generalists. Redundancy analysis (RDA) and variance partitioning analysis (VPA) results revealed that the contribution of the interaction between soil physicochemical parameters and soil enzymes was greater than their individual contributions. In summary, this study is the first to elucidate the microbial diversity and community structure of L. chinensis and compare the diversity and composition between rhizospheric and endosphere microbiomes.

Exploring the effects of volcanic eruption disturbances on the soil microbial communities in the montane meadow steppe.

Volcanic eruptions are important components of natural disturbances that provide a model to explore the effects of volcanic eruption disturbances on soil microorganisms. Despite widespread research, to the best of our knowledge, no studies of volcanic eruption disturbances have investigated the effects on soil microbial communities in the montane meadow steppe. To address this gap, we meticulously investigated the characteristics of the soil microbial communities from the volcano and steppe sites using Illumina MiSeq high-throughput sequencing. Hierarchical clustering analysis and principal coordinate analysis (PCoA) showed that the soil microbial communities from the volcano and steppe sites differed. The diversity and richness of the soil microbial communities from the steppe sites were significantly higher than at the volcano sites (P < 0.05), and the soil microbial communities in the steppe sites had higher stability. The effects of volcanic eruption disturbances on the bacterial community development are greater than its effects on the fungal communities. The environmental filtering of volcanic eruptions selectively retained some special microorganisms (i.e., Conexibacter, Agaricales, and Gaiellales) with strong adaptability to the environmental disturbances, enhanced metabolic activity for sodium and calcium reabsorption, and increased relative abundances of the lichenized saprotrophs. The soil microbial communities from the volcano and steppe sites cooperate to form complex networks of species interactions, which are strongly influenced by the interaction of the soil and vegetation factors. Our findings provide new information on the effects of volcanic eruption disturbances on the soil microbial communities in the montane meadow steppe.