Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage.

Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.

[Distribution Pattern of Bacterial Community in Soil Profile of Larix principis-rupprechtii Forest in Luya Mountain].

Microbial communities are the key component to maintaining the structure and function of forest soil ecosystems. The vertical distribution of bacterial communities on the soil profile has an important impact on forest soil carbon pools and soil nutrient cycling. Using Illumina MiSeq high-throughput sequencing technology, we analyzed the characteristics of bacterial communities in the humus layer and 0-80 cm soil layer of Larix principis-rupprechtii in Luya Mountain, China, to explore the driving mechanisms affecting the structure of bacterial communities in soil profiles. The results showed that the α diversity of bacterial communities decreased significantly with increasing soil depth, and community structure differed significantly across soil profiles. The relative abundance of Actinobacteria and Proteobacteria decreased with increased soil depth, whereas the relative abundance of Acidobacteria and Chloroflexi increased with the increase in soil depth. The results of RDA analysis showed that soil NH+4, TC, TS, WCS, pH, NO-3, and TP were important factors determining the bacterial community structure of the soil profile, among which soil pH had the most significant effect. Molecular ecological network analysis showed that the complexity of bacterial communities in the litter layer and subsurface soil (10-20 cm) was relatively high, whereas the complexity of bacterial communities in deep soil (40-80 cm) was relatively low. Proteobacteria, Acidobacteria, Chloroflexi, and Actinobacteria played important roles in the structure and stability of soil bacterial communities in Larch. The species function prediction of Tax4Fun showed a gradual decline in microbial metabolic capacity along the soil profile. In conclusion, soil bacterial community structure showed a certain distribution pattern along the vertical profile of soil, the community complexity gradually decreased, and the unique bacterial groups of deep soil and surface soil were significantly different.

Distribution patterns and driving mechanism of soil protozoan community at the different depths of Larix principis-chinensis forest in the Luya Mountain, China.

To reveal the assembly mechanisms of soil protozoan community in subalpine forest ecosystems, we analyzed the composition and diversity of protozoan communities and their drivers at the six strata (the litter profile, humus profile, 0-10 cm, 10-20 cm, 20-40 cm and 40-80 cm) of soil profiles in subalpine Larix principis-rupprechtii forest in Luya Mountain using Illumina Miseq high-throughput sequencing technology. The results showed that protozoa in the soil profiles belonged to 335 genera, 206 families, 114 orders, 57 classes, 21 phyla, and 8 kingdoms. There were five dominant phyla (relative abundance >1%) and 10 dominant families (relative abundance >5%). The α diversity decreased significantly with increasing soil depth. Results of PCoA analysis showed that the spatial composition and structure of protozoan community differed significantly across soil depths. The results of RDA analysis showed that soil pH and soil water content were important factors driving protozoan community structure across soil profile. Null model analysis suggested that the heterogeneous selection dominated the processes of protozoan community assemblage. Molecular ecological network analysis revealed that the complexity of soil proto-zoan communities decreased continuously with increasing depth. These results elucidate the assembly mechanism of soil microbial community in subalpine forest ecosystem.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development.

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Dynamics Relationship of Phyllosphere and Rhizosphere Bacterial Communities During the Development of Bothriochloa ischaemum in Copper Tailings.

Copper mining and the byproducts associated with the industry have led to serious pollution in the Loess Plateau of China. There is a potential in improving the ecological restoration efficiency of such degraded land through combining microbial and plant remediation approaches. However, the community structure and function of phyllosphere and rhizosphere microorganisms and their response to plant development in copper tailings dams are poorly understood. This study investigated the impact of the phyllosphere and rhizosphere microbial communities on Bothriochloa ischaemum during three distinct plant development stages: seedling, tiller, and mature. The relative species abundance and Shannon index of bacterial communities of the rhizosphere during the seedling and tiller stages were distinct from that in the mature stage. Dominant bacteria at the level of phyla, such as Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes, followed distinct patterns associated with plant development in the phyllosphere, but the predominant bacteria were similar in the rhizosphere. Redundancy analysis showed that aboveground total nitrogen and the carbon and nitrogen ratio of this plant species significantly affected phyllosphere bacterial community structure, whereas soil water content, soil nutrients, electrical conductivity, and salinity significantly affected rhizosphere bacterial community structure. Moreover, keystone phyllosphere and rhizosphere bacterial species differed significantly. This study sheds new light on understanding the dynamic relationship of phyllosphere and rhizosphere bacterial communities during plant development in copper tailings. These results are beneficial to the development and utilization of beneficial microbial communities at different stages of development, which might help to reclaim and stabilize tailings more effectively.

Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China.

Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO3--N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation.IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.

Effects of the integration of mixed-cropping and rice-duck co-culture on rice yield and soil nutrients in southern China.

BACKGROUND: Biodiversity-based agricultural systems can improve production efficiency and sustainability, with fewer negative environmental impacts and lower use of external inputs. Mixed-cropping and rice-duck co-culture have been shown to produce ecological benefits and to have positive effects on paddy soil. However, the effects of a combination of mixed cropping with different rice cultivars and duck co-culture on soil nutrients availability and grain yields have not been evaluated. A paddy field experiment was carried out over two rice growing seasons to test these effects. RESULTS: Several combinations of rice cultivars, when integrated with duck co-culture, significantly increased the soil organic matter and total nitrogen contents during the rice growing seasons, as compared to mono-cropping systems. In mixed-cropping combined with duck co-culture (MCDC) systems, the soil alkali-hydrolyzable nitrogen content ranged from 4.33% to 17.86% higher than that in mono-cropping systems. Similar increases were found for soil available phosphorus (8.71-15.91%) and soil available potassium (8.65-39.43%) contents. Furthermore, MCDC produced higher grain yields and harvest indexes for both study seasons. CONCLUSION: The integration of MCDC systems had positive effects on soil nutrient contents of paddy fields, which could, in turn, lead to yield enhancements, as well as additional income for farmers in the form of organic duck meat. © 2019 Society of Chemical Industry.

Dual-Functional Antifogging/Antimicrobial Polymer Coating.

Dual-functional antifogging/antimicrobial polymer coatings were prepared by forming a semi-interpenetrating polymer network (SIPN) of partially quaternized poly(2-(dimethylamino)ethyl methacrylate-co-methyl methacrylate) and polymerized ethylene glycol dimethacrylate network. The excellent antifogging behavior of the smooth coating was mainly attributed to the hydrophilic/hydrophobic balance of the partially quaternized copolymer, while the covalently bonded, hydrophobic quaternary ammonium compound (5 mol % in the copolymer) rendered the coating strongly antimicrobial, as demonstrated by the total kill against both Gram-positive Staphylococcus epidermidis and Gram-negative Escherichia coli. The antimicrobial action of the SIPN coating was based on contact killing, without leaching of bactericidal species, as revealed by a zone-of-inhibition test. This type of dual-functional coating may find unique applications where both antimicrobial and antifogging properties are desired.

Self-Stratified Antimicrobial Acrylic Coatings via One-Step UV Curing.

We designed and synthesized a novel quaternary ammonium methacrylate compound (QAC-2) bearing a perfluoroalkyl tail on one end and an acrylic moiety on the other. Via one-step UV curing of QAC-2 and methyl methacrylate (MMA) with ethylene glycol dimethacrylate (EGDMA) as the cross-linker, we obtained cross-linked coatings with excellent antimicrobial property, as demonstrated by the total kill against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus epidermidis (S. epidermidis) at a QAC-2 concentration as low as ∼0.06 mol % (∼0.4 wt %) relative to MMA, which was substantially lower than the QAC amount needed in the coatings containing QACs with a hydrocarbon tail. A zone of inhibition test confirmed that the antimicrobial effect was on the basis of contact killing and there was no leaching of antimicrobial species from the cross-linked coating. The high antimicrobial potency in QAC-2-containing films was the consequence of strong surface enrichment of the fluorinated QAC, as confirmed by X-ray photoelectron spectroscopy (XPS).

Bacterial community in the biofilm of granular activated carbon (GAC) PreBiofilter in bench-scale pilot plants for surface water pretreatment.

Biofilters of granular activated carbon (GAC) are responsible for the removal of organic matters in drinking water treatments. PreBiofilters, which operate as the first unit in a surface water treatment train, are a cost-effective pretreatment for conventional surface water treatment and provide more consistent downstream water quality. This study investigated bacterial communities from the samples of raw surface water, biofilm on the PreBiofilter, and filtrates for surface water pretreatment. A bench-scale pilot plant of PreBiofilter was constructed to pretreat surface water from the Canoochee River, GA, USA. PreBiofilter exhibited a significant reduction of total organic carbon and dissolved organic carbon. The evenness and Shannon diversity of bacterial operational taxonomic units (OTUs) were significantly higher on the biofilm of PreBiofilter than in raw water and filtrates. Similar bacteria communities were observed in the raw water and filtrates using relative abundance of bacterial OTUs. However, the bacterial communities in the filtrates became relatively similar to those in the biofilm using presence/absence of bacterial OTUs. GAC biofilm or raw water and filtrates greatly contributed to the abundance of bacteria; whereas, bacteria sheared from colonized biofilm and entered filtrates. Evenly distributed, diverse and unique bacteria in the biofilm played an important role to remove organic matters from surface water for conventional surface water pretreatment.

Biological impact of divergent land management practices on tomato crop health.

Development of sustainable food systems is contingent upon the adoption of land management practices that can mitigate damage from soilborne pests. Five diverse land management practices were studied for their impacts on Fusarium wilt (Fusarium oxysporum f. sp. lycopersici), galling of roots by Meloidogyne spp. and marketable yield of tomato (Solanum lycopersicum) and to identify associations between the severity of pest damage and the corresponding soil microbial community structure. The incidence of Fusarium wilt was >14% when tomato was cultivated following 3 to 4 years of an undisturbed weed fallow or continuous tillage disk fallow rotation and was >4% after 3 to 4 years of bahiagrass (Paspalum notatum) rotation or organic production practices that included soil amendments and cover crops. The incidence of Fusarium wilt under conventional tomato production with soil fumigation varied from 2% in 2003 to 15% in 2004. Repeated tomato cultivation increased Fusarium wilt by 20% or more except when tomato was grown using organic practices, where disease remained less than 3%. The percent of tomato roots with galls from Meloidogyne spp. ranged from 18 to 82% in soil previously subjected to a weed fallow rotation and 7 to 15% in soil managed previously as a bahiagrass pasture. Repeated tomato cultivation increased the severity of root galling in plots previously subjected to a conventional or disk fallow rotation but not in plots managed using organic practices, where the percentage of tomato roots with galls remained below 1%. Marketable yield of tomato exceeded 35 Mg ha(-1) following all land management strategies except the strip-tillage/bahiagrass program. Marketable yield declined by 11, 14, and 19% when tomato was grown in consecutive years following a bahiagrass, weed fallow, and disk rotation. The composition of fungal internal transcribed spacer 1 (ITS1) and bacterial 16S rDNA amplicons isolated from soil fungal and bacterial communities corresponded with observed differences in the incidence of Fusarium wilt and severity of root galling from Meloidogyne spp. and provided evidence of an association between the effect of land management practices on soil microbial community structure, severity of root galling from Meloidogyne spp., and the incidence of Fusarium wilt.

Molecular study of worldwide distribution and diversity of soil animals.

The global distribution of soil animals and the relationship of below-ground biodiversity to above-ground biodiversity are not well understood. We examined 17,516 environmental 18S rRNA gene sequences representing 20 phyla of soil animals sampled from 11 locations covering a range of biomes and latitudes around the world. No globally cosmopolitan taxa were found and only 14 of 2,259 operational taxonomic units (OTUs) found were common to four or more locations. Half of those were circumpolar and may reflect higher connectivity among circumpolar locations compared with other locations in the study. Even when OTU assembly criteria were relaxed to approximate the family taxonomic level, only 34 OTUs were common to four or more locations. A comparison of our diversity and community structure data to environmental factors suggests that below-ground animal diversity may be inversely related to above-ground biodiversity. Our data suggest that greater soil inorganic N and lower pH could explain the low below-ground biodiversity found at locations of high above-ground biodiversity. Our locations could also be characterized as being dominated by microarthropods or dominated by nematodes. Locations dominated by arthropods were primarily forests with lower soil pH, root biomass, mean annual temperature, low soil inorganic N and higher C:N, litter and moisture compared with nematode-dominated locations, which were mostly grasslands. Overall, our data indicate that small soil animals have distinct biogeographical distributions and provide unique evidence of the link between above-ground and below-ground biodiversity at a global scale.

Comparison of soil bacterial communities under diverse agricultural land management and crop production practices.

The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.

Exploring interactions between saprotrophic microbes and ectomycorrhizal fungi using a protein-tannin complex as an N source by red pine (Pinus resinosa).

• Recent studies suggest that some plants may circumvent N mineralization carried out by saprotrophs because their ectomycorrhizal fungi have the capacity to hydrolyse protein. When complexed by tannins, however, proteins may be unavailable to some ectomycorrhizal fungi. • Here we tested the hypothesis that when protein-tannin complex is the N source, Pisolithus tinctorius will promote N uptake into red pine (Pinus resinosa) only in the presence of saprotrophs. • The model protein-tannin complex was stable at field pH. P. tinctorius could not obtain N from it, but saprotrophs could. Pre-treatment of the complex by saprotrophs did make its N available to ectomycorrhizal fungi. However, when the protein-tannin complex was the major N source, P. tinctorius increased shoot P but not N content, even in the presence of saprotrophs. • Interactions between saprotrophs and ectomycorrhizal fungi may be different for N and P because of immobilization of N by ectomycorrhizal fungi, or by the more rapid diffusion of ammonium than phosphate, rendering the absorptive surface area of ectomycorrhizal fungi superfluous for uptake of N but not for P.