Inconsistent response of soil bacterial and fungal communities in aggregates to litter decomposition during short-term incubation

Fungal diversity and key functional gene abundance in Iowa bioretention cells: implications for stormwater remediation potential

Stormwater bioretention cells are green stormwater infrastructure systems that can help mitigate flooding and remove contaminants. Plants and bacteria improve nutrient removal and degrade organic contaminants; however, the roles of fungi in bioretention cells are less known. Although mycorrhizal fungi aid in plant growth/improve nutrient uptake, there is a notable lack of research investigating fungal diversity in bioretention cells. Other types of fungi could benefit bioretention cells (e.g., white rot fungi degrade recalcitrant contaminants). This study addresses the knowledge gap of fungal function and diversity within stormwater bioretention cells. We collected multiple soil samples from 27 different bioretention cells in temperate-climate eastern Iowa USA, characterized soil physicochemical parameters, sequenced the internal transcribed spacer (ITS) amplicon to identify fungal taxa from extracted DNA, and measured functional gene abundances for two fungal laccases (Cu1, Cu1A) and a fungal nitrite reductase gene (nirKf). Fungal biodegradation functional genes were present in bioretention soils (mean copies per g: 7.4 × 105nirKf, 3.2 × 106Cu1, 4.0 × 108Cu1A), with abundance of fungal laccase and fungal nitrite reductase genes significantly positively correlated with soil pH and organic matter (Pearson's R: >0.39; rho < 0.05). PERMANOVA analysis determined soil characteristics were not significant explanatory variables for community composition (beta diversity). In contrast, planting specifications significantly impacted fungal diversity; the presence/absence of a few planting types and predominant vegetation type in the cell explained 89% of variation in fungal diversity. These findings further emphasize the importance of plants and media as key design parameters for bioretention cells, with implications for fungal bioremediation of captured stormwater contaminants.

Macroaggregates Serve as Micro-Hotspots Enriched With Functional and Networked Microbial Communities and Enhanced Under Organic/Inorganic Fertilization in a Paddy Topsoil From Southeastern China

Microbial communities of soil aggregate-size fractions were explored with molecular and networking assays for topsoil samples from a clayey rice paddy under long-term fertilization treatments. The treatments included no fertilizer (NF) as control, chemical fertilizer only (CF), chemical fertilizer with swine manure (CFM), and chemical fertilizer with rice straw return (CFS). Following a wet-sieving protocol, water-stable aggregates were separated into size fractions of large macroaggregates (L-MacA, >2,000 μm), macroaggregates (MacA, 2,000-250 μm), microaggregates (MicA, 250-53 μm), fine microaggregates (F-MicA, 53-2 μm), and fine clay (F-Clay, <2 μm). Mass proportion was 32.3-38.2% for F-MicA, 23.0-31.5% for MacA, 19.0-23.1% for MicA, 9.1-12.0% for L-MacA, and 4.9-7.5% for F-Clay, respectively. The proportion of MacA was increased, but F-Clay was reduced by fertilization, whereas the mean weight diameter was increased by 8.0-16.2% from 534.8 μm under NF to 621.5 μm under CFM. Fertilization affected bacterial 16S rRNA and fungal 18S rRNA gene abundance in F-MicA and F-Clay but not in aggregates in size larger than 53 μm. However, bacterial and fungal community α-diversities and community structures were quite more divergent among the fertilization treatments in all size fractions. Organic carbon and gene abundance of bacteria and fungi were enriched in both L-MacA and MacA but depleted in F-Clay, whereas microbial Shannon diversity was rarely changed by fraction size under the four treatments. L-MacA and MacA contained more bacteria of r-strategists and copiotrophs, whereas F-MicA and F-Clay were demonstrated with a higher abundance of K-strategists and oligotrophs. Guilds of parasitic and litter saprotrophic fungi were enriched in F-MicA but depleted in L-MacA. Furthermore, most of bacterial and fungal operational taxonomic units were strongly interacted in L-MacA and MacA rather than in MicA and F-Clay. Thus, MacA acted as micro-hotspots enriched with functional and networked microbial communities, which were enhanced with organic/inorganic fertilization in the rice paddy.

Inconsistent response of bacterial phyla diversity and abundance to soil salinity in a Chinese delta

Soil salinization is an increasingly serious problem and decreases crop yields in the Yellow River Delta (YRD), but its effects on bacterial community and diversity at the phylum level are not well known. We used high-throughput sequencing of soil bacterial 16S rRNA to identify soil bacterial communities and diversity across a gradient of soil salinity (electrical conductivity), namely, S1: low salinity level (1.78 ds/m), S2: medium salinity level (3.16 ds/m), S3: high salinity level (17.26 ds/m), S4: extreme salinity level (34.41 ds/m), and a non-salted site as the control (CK, 0.92 ds/m). Our results indicated the significantly higher values of soil C/N ratio in S2, S3, and S4 compared with that in CK. Significantly lower values of the Shannon and Chao 1 indexes were observed in S4 compared with the CK (p < 0.05). High salinity decreased the relative abundance of Actinobacteria and Acidobacteria, but increased that of Gemmatimonadetes and Bacteroidetes. Additionally, the Shannon diversity of Bacteroidetes increased by 15.5% in S4 compared with that in the CK. Our results indicate that soil salt is a main factor regulating bacterial phyla diversity and community in the extremely saline-alkaline soils of YRD. The high abundance and diversity of Bacteroidetes can be used for saline-alkali land restoration.

Soil degradation influences soil bacterial and fungal community diversity in overgrazed alpine meadows of the Qinghai-Tibet Plateau

Over half of the alpine meadows in the Qinghai-Tibet Plateau (QTP) are degraded due to human activities. Soil degradation from overgrazing is the most direct cause of grassland degradation. It is thus important to synthesize the effects of multiple soil degradation indicators on the belowground biomass of plants and soil microorganisms in the degraded QTP. We studied the diversities and structures of soil bacterial and fungal communities using soil bacterial 16S rRNA and the fungal ITS gene under four degradation gradients, D1: lightly degraded, D2: moderately degraded, D3: highly degraded, and a non-degraded control site (CK). The bacterial Shannon diversity in D3 was significantly lower than that in D1 (p < 0.001), and the bacterial richness index in D3 was significantly lower than that in D1 (p < 0.001). There was no difference in soil fungal diversity among the different degradation levels; however, soil fungal richness decreased significantly from CK to D3. The phyla Actinobacteria, Acidobacteria and the genus Mortierella were differed significantly under the four degradation gradients. Plant litter mass and root C/N ratio were important factors associated with bacterial and fungal diversity and richness. These results indicated that alpine meadow degradation can lead to variations in both microbial diversity and the potential functioning of micro-organisms in the QTP.

Soil Salinity Drives the Distribution Patterns and Ecological Functions of Fungi in Saline-Alkali Land in the Yellow River Delta, China

High soil salinity is the main factor that limits soil microbial activity in the Yellow River Delta (YRD); however, its effects on fungal community and ecological function are unknown. Here, we comparatively investigated the diversity and structures of soil fungal communities targeting the internally transcribed fungal spacer gene using Illumina MiSeq sequencing methods under a salt gradient with five levels, namely, Low: low-salinity soil, Medium: medium-salinity soil, High: high-salinity soil, Extreme: extreme-salinity soil, and a non-salted site as the control (Non-saline). The results show that bulk density (BD) values significantly increased (p < 0.05), while significantly lower values of soil total carbon (TC), total nitrogen (TN), and fungal Shannon and Chao indexes were observed as the salinization gradient increased (p < 0.05). The relatively high levels of the families Nectriaceae and Cladosporiaceae distinguished two of the clusters, indicating two enterotypes of low (Non-saline and Low) and high (Medium, High, and Extreme) salinity soils, respectively. The family Nectriaceae was most abundant in the networks, and the positive correlations were more pronounced than negative correlations; however, Cladosporiaceae was the family most negatively correlated with others based on the network analysis. At the ecological function level, plant saprotrophs and litter saprotroph were significantly less abundant in extremely saline soil than non-saline soil. The change in soil properties (TC, TN, and BD) caused by soil salinization [salt and electrical conductivity (EC)] regulated the diversity of soil fungal communities, and ecological function, as indicated by Pearson correlation analyses. We suggest further investigation into the ecological functions of soil microorganisms in the extremely saline-alkaline soils of the YRD.

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.