[Characteristics of Epiphytic Bacterial Community on Submerged Macrophytes in Water Environment Supplemented with Reclaimed Water]

Biofilms attached to submerged macrophytes play an important role in improving the water quality of the water environment supplemented with reclaimed water. In order to explore the effects of reclaimed water quality and submerged macrophyte species on the characteristics of an epiphytic bacterial community, different types of submerged macrophytes were selected as research objects in this study. 16S rRNA high-throughput sequencing technology was used on the epiphytic bacteria and the surrounding environmental samples to analyze the bacterial community structure and functional genes. The results showed that approximately 20%-35% of the nitrogen and phosphorus nutrients were absorbed and utilized in the water environment supplemented with reclaimed water. However, the COD, turbidity, and chroma of the downstream water were significantly increased. The bacterial community of the biofilms attached to submerged macrophytes was significantly different from that in the surrounding environment (soil, sediment, and water body) and in the activated sludge that was treated by reclaimed water. In terms of bacterial community diversity, the richness and diversity were significantly lower than those of soil and sediment but higher than those of plankton bacteria in water. In terms of bacterial community composition, dominant genera and corresponding abundances were also different from those of other samples. The main dominant bacterial genera were Sphingomonas, Aeromonas, Pseudomonas, and Acinetobacter, accounting for 7%-40%, respectively. Both macrophyte species and the quality of reclaimed water (BOD5, TN, NH4+-N, and TP) could affect the bacterial community. However, the effect of water quality of the bacterial community was greater than that of macrophytes species. Additionally, the quality of reclaimed water also affected the abundance of functional genes in the bacterial community, and the relative abundance of nitrogen and phosphorus cycling functional genes was higher in areas with higher nitrogen and phosphorus concentrations.

Seasonal Changes in the Soil Microbial Community Structure in Urban Forests

Urban forests play a crucial role in the overall health and stability of urban ecosystems. Soil microorganisms are vital to the functioning of urban forest ecosystems as they facilitate material cycling and contribute to environmental stability. This study utilized high-throughput sequencing technology to examine the structural characteristics of bacterial and fungal communities in the bulk soil of six different forest stands: Phyllostachys pubescens (ZL), Metasequoia glyptostroboides (SSL), Cornus officinalis (SZY), mixed broad-leaved shrub forest (ZKG), mixed pine and cypress forest (SBL), and mixed broad-leaved tree forest (ZKQ). Soil samples were collected from each forest stand, including the corners, center, and edges of each plot, and a combined sample was created from the first five samples. The results revealed that among the bacterial communities, ZKG exhibited the highest alpha diversity in spring, while ZL demonstrated the highest alpha diversity in both summer and autumn. Proteobacteria was the most abundant bacterial phylum in all six forest stand soils. The dominant fungal phylum across the six forest stands was identified as Ascomycota. Notably, the microbial community diversity of SBL bulk soil exhibited significant seasonal changes. Although ZL exhibited lower bacterial community diversity in spring, its fungal community diversity was the highest. The bulk soil microbial diversity of ZL and SSL surpassed that of the other forest stands, suggesting their importance in maintaining the stability of the urban forest ecosystem in the Zhuyu Bay Scenic Area. Furthermore, the diversity of the bulk soil microbial communities was higher in all six stands during spring compared to summer and autumn. Overall, this study provides valuable insights into the seasonal variations of bulk soil microbial communities in urban forests and identifies dominant tree species, offering guidance for tree species' selection and preservation in urban forest management.

Effects of yak and Tibetan sheep grazing on soil arthropods community in an alpine meadow on the Qinghai-Tibet Plateau, China

We investigated the responses of community structure of soil arthropods to yak and Tibetan sheep grazing based on a manipulated grazing experiment at the alpine meadow livestock Adaptive Management Platform, which locates in Haiyan County, Qinghai Province. The results showed that the obtained soil arthropods belonged to 26 families, 8 orders, and 4 classes, with Acaroidae and Oribatida as the dominant groups. Yak and Tibetan sheep grazing decreased the abundance but increased Shannon index, Margalef index and Pielou index of soil arthropods. Yak grazing significantly increased the quantity of the predatory soil arthropod groups. Yak and Tibetan sheep gra-zing significantly increased the quantity of the detritivore soil arthropod groups, but did not affect the quantity of the omnivorous and phytophagous soil arthropod groups. Yak and Tibetan sheep grazing significantly reduced the abundance of soil mites. Soil bulk density, available potassium, and available nitrogen were the main abiotic factors affecting soil arthropods community composition.

Potential short-term effects of earthquake on the plant-soil interface in alpine grassland of the Qinghai-Tibetan Plateau

Earthquakes are environmental disturbances affecting ecosystem functioning, health, and biodiversity, but their potential impacts on plant-soil interface are still poorly understood. In this study, grassland habitats in areas near and away from the seismo-fault in Madou, a region typical of alpine conditions on the Qinghai-Tibetan Plateau, were randomly selected. The impacts of earthquake on soil properties and plant nutrient content in the short term were emphasized, and their potential relationships with community diversity and productivity were examined. According to the findings of the study, the Maduo earthquake led to a decrease in soil nutrient content in alpine grassland ecosystems, especially soil TC, TN, TP, TCa, AP, AK, NH4 +-N, and SOC, and inhibited the absorption of N, Ca, and Mg nutrients by plants. In addition, the diversity and productivity of communities were affected by both direct and indirect earthquake pathways. The negative impacts of seismic fracture on soil structure had the most significant direct impact on plant community diversity. Earthquakes also indirectly reduced community productivity by reducing the soil N content and inhibiting the absorption of plant nutrients. Our findings suggested that earthquakes could potentially decrease the stability of the alpine grassland ecosystem on the QTP by affecting nutrient availability at the plant-soil interface.

Intraspecific variation in a predator changes intertidal community through effects on a foundation species

Intraspecific variation is an important form of biodiversity that can alter community and ecosystem properties. Recent work demonstrates the community effects of intraspecific variation in predators via altering prey communities and in foundation species via shaping habitat attributes. However, tests of the community effects of intraspecific trait variation in predators acting on foundation species are lacking despite the fact that consumption of foundation species can have strong community effects by shaping habitat structure. Here, we tested the hypothesis that intraspecific foraging differences among populations of mussel-drilling dogwhelk predators (Nucella) differentially alter intertidal communities through effects on foundational mussels. We conducted a 9-month field experiment where we exposed intertidal mussel bed communities to predation from three Nucella populations that exhibit differences in size-selectivity and consumption time for mussel prey. At the end of the experiment, we measured mussel bed structure, species diversity, and community composition. While exposure to Nucella originating from different populations did not significantly alter overall community diversity, we found that differences in Nucella mussel selectivity significantly altered foundational mussel bed structure, which in turn altered the biomass of shore crabs and periwinkle snails. Our study extends the emerging paradigm of the ecological importance of intraspecific variation to include the effects of intraspecific variation on predators of foundation species.

[Effects of the Transformation from Natural Alpine Grassland to Mixed Artificial Grassland on the Characteristics of Soil Microbial Community]

This study aimed to analyze the effects of the transformation from natural alpine grassland (NAG) to mixed artificial grassland (MAG) on the characteristics of soil microbial community. We used Illumina Miseq high-throughput sequencing technology to investigate the soil microbial community of natural grassland and mixed artificial grassland. The results showed that plant diversity and the content of soil organic matter decreased significantly from NAG to MAG. In total, 29 and 11 phyla bacteria and fungi were detected, respectively. Compared with that in NAG, the Shannon indexes of the bacterial community increased significantly in MAG (from 9.51 to 9.89), whereas these differences were not significant between the NAG and MAG fungal community. The structure and composition of the soil microbial community showed significant differences between NAG and MAG. In addition, Mantel test results suggested that soil total organic matter, total nitrogen, and soil moisture were significantly correlated with variations in the bacterial community, and soil total organic matter and soil moisture were significantly correlated with variations in fungal community. The results of linear discriminant analysis (LEfSe) indicated that Atribacteria and Ascomycota microorganisms could be considered as the indicator groups for NAG, whereas Gemmata and Trichocomaceae microorganisms could be considered as the indicator groups for MAG. Tax4Fun2 results showed that the transition from NAG to MAG affected the utilization of different carbon sources by bacteria.

[Characteristics of Soil Microbial Community in Different Habitats in the Process of Ecological Restoration of Haifeng Wetland in Guangdong]

Soil microorganisms can respond to changes in wetland ecosystem quality and functional evolution sensitively. To explore the changes and response mechanisms of soil microorganisms under ecological restoration measures, the characteristics of the soil microbial community and their influencing factors were analyzed using high-throughput sequencing technology in four different habitats (revegetation area, native vegetation area, tidal creek, and tidal flat) during the ecological restoration process in Haifeng wetland in Guangdong. The results showed that:soil physicochemical properties of the four different habitats were significantly different; the contents of TC, TN, TOC, and TK in the tidal creek were significantly higher than those in the other habitats; and the contents of TC, TN, and TP in the revegetation restoration area were significantly higher than those in the tidal flat. The EC values in the tidal creeks and tidal flat were significantly higher than those in the revegetation area and the native vegetation area. The diversity index and abundance of soil bacteria in the tidal creek were the highest, and those in the vegetation restoration area were significantly higher than those in the bare flat. The archaea in the tidal creek were significantly more complex than those in the other three habitats, and the fungal community diversity index and abundance in the native vegetation area were significantly higher than those in the other areas, which had the most complex community structure. TN and TC were the main factors affecting the bacterial community, whereas TN and EC were the main factors affecting the archaea community, and pH, TN, and TP were the key factors affecting the fungal community. In conclusion, the planting of vegetation on the tidal flat increased the diversity and richness of the soil microbial community during the process of ecological restoration, indicating that it has resulted in positive feedback on ecological restoration so far. The results of this study can provide a theoretical basis for the selection of ecological restoration strategies for the tidal flat.

Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China

Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long-term selection pressures.

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.

[Effects of Simulated Acid Rain and Nitrogen Deposition on Soil Bacterial Community Structure and Diversity in the Masson Pine Forest]

By analyzing the effects of acid rain and nitrogen deposition on the structure and diversity of soil bacterial communities, the response mechanism of Masson pine forests to environmental stress was investigated, providing a theoretical reference basis for resource management and conservation in Tianmu Mountain National Nature Reserve. Four treatments of the simulated acid rain and nitrogen deposition were set up in 2017 to 2021 in Tianmu Mountain National Nature Reserve (pH value of 5.5 and 0 kg·(hm²·a)^-1, CK; pH value of 4.5 and 30 kg·(hm²·a)^-1, T1; pH value of 3.5 and 60 kg·(hm²·a)^-1, T2; pH value of 2.5 and 120 kg·(hm²·a)^-1, T3). The differences in soil bacterial community composition and structure among treatments and their influencing factors were analyzed by collecting soils from four treatments, using the Illumina MiSeq PE300 second-generation high-throughput sequencing platform. The results showed that acid rain and nitrogen deposition significantly reduced soil bacterial α-diversity (P<0.05) in a Masson pine forest. The Masson pine forest soils consisted of 36 phylum groups of mycota, with Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi as the main bacterial phyla (relative abundance>1%) in the Masson pine forest soils. Flavobacterium, Nitrospira, Haliangium, Candidatus_Koribacter, Bryobacter, Occallatibacter, Acidipla, Singulisphaera, Pajaroellobacter, and Acidothermus, which showed significant changes in relative abundance under the four treatments, could be used as indicator species for changes in soil bacterial communities under acid rain and nitrogen deposition stress. Soil pH and total nitrogen were influential factors in the diversity of soil bacterial communities. As a result, acid rain and nitrogen deposition increased the potential ecological risk, and the loss of microbial diversity will change the ecosystem function as well as reduce the stability of the ecosystem.

The multiscale feedback theory of biodiversity

Plants and their environments engage in feedback loops that not only affect individuals, but also scale up to the ecosystem level. Community-level negative feedback facilitates local diversity, while the ability of plants to engineer ecosystem-wide conditions for their own benefit enhances local dominance. Here, we suggest that local and regional processes influencing diversity are inherently correlated: community-level negative feedback predominates among large species pools formed under historically common conditions; ecosystem-level positive feedback is most apparent in historically restricted habitats. Given enough time and space, evolutionary processes should lead to transitions between systems dominated by positive and negative feedbacks: species-poor systems should become richer due to diversification of dominants and adaptation of subordinates; however, new monodominants may emerge due to migration or new adaptations.

Phytoplankton Community Response to Environmental Factors along a Salinity Gradient in a Seagoing River, Tianjin, China

A river-estuary ecosystem usually features a distinct salinity gradient and a complex water environment, so it is enormously valuable to study the response mechanism of living organisms to multiple abiotic factors under salinity stress. Phytoplankton, as an important part of aquatic microorganisms, has always been of concern for its crucial place in the aquatic ecosystem. In this study, phytoplankton data and 18 abiotic factors collected from 15 stations in Duliujian River, a seagoing river, were investigated in different seasons. The results showed that the river studied was of a Cyanophyta-dominant type. Salinity (SAL) was the key control factor for phytoplankton species richness, while water temperature (WT) was critical not only for species richness, but also community diversity, and the abundance and biomass of dominant species. Apart from WT, the abundance and biomass of dominant species were also driven by total nitrogen (TN), nitrate (NO₃^-), pH, and water transparency (SD). Moreover, total dissolved phosphorus (TDP), pH, and chemical oxygen demand (COD) were crucial for community diversity and evenness. The bloom of dominant species positively associated with TDP led to lower diversity and evenness in autumn. In addition, when available nitrogen was limited, Pseudoanabaena sp. could obtain a competitive advantage through the N₂ fixation function. Increased available nitrogen concentration could favor the abundance of Chlorella vulgaris to resist the negative effect of WT. The results show that Oscillatoria limosa could serve as an indicator of organic contamination, and nutrient-concentration control must be effective to inhibit Microcystis bloom. This could help managers to formulate conservation measures.

Short-Term Vegetation Restoration Enhances the Complexity of Soil Fungal Network and Decreased the Complexity of Bacterial Network

Different vegetation restoration methods may affect the soil’s physicochemical properties and microbial communities. However, it is not known how the microbial network’s complexity of the bacterial and fungal communities respond to short-term vegetation restoration. We conducted a short-term ecological restoration experiment to reveal the response of the soil’s microbial community and microbial network’s stability to initial vegetation restoration during the restoration of the degraded grassland ecosystem. The two restoration methods (sowing alfalfa (Medicago sativa, AF) and smooth brome (Bromus inermis, SB)) had no significant effect on the alpha diversity of the fungal community, but the SB significantly increased the alpha diversity of the soil surface bacterial community (p < 0.01). The results of NMDS showed that the soil’s fungal and bacterial communities were altered by a short-term vegetation restoration, and they showed that the available phosphorus (AP), available potassium (AK), and nitrate nitrogen (nitrate-N) were closely related to changes in bacterial and fungal communities. Moreover, a short-term vegetation restoration significantly increased the complexity and stability of fungi ecological networks, but the opposite was the case with the bacteria. Our findings confirm that ecological restoration by sowing may be favorable to the amelioration of soil fungi complexity and stability in the short-term. Such findings may have important implications for soil microbial processes in vegetation recovery.

Impacts of corn intercropping with soybean, peanut and millet through different planting patterns on population dynamics and community diversity of insects under fertilizer reduction

Corn is one of the key grain crops in China and the excessive use of chemical fertilizers and pesticides seriously damages the ecological environment in fields. To explore a more scientific and reasonable way to plant corn and simultaneously reduce the overuse of chemical fertilizers and pesticides, the impact of corn intercropping with soybean, peanut, and millet, respectively, through five planting patterns, including three intercropping patterns (2 corn rows to 2, 3 and 4 rows of soybean/peanut or 2, 4 and 6 millet rows, respectively) and two monoculture patterns of corn and soybean, peanut or millet under normal (600 kg/ha) and reduced (375 kg/ha) levels of NPK (N:P₂O₅:K₂O = 15:15:15) fertilization on the population abundance and community diversity of insects, leaf nutrients, and induced plant hormones jasmonic acid (JA) and salicylic acid (SA) was studied in 2018 and 2019. The results showed that the insect community indexes of the species number (S), the diversity index (H), and the uniformity index (E) generally increased under intercropping and were significantly higher than those under corn monoculture. The prevalence of Asian corn borer (Ostrinia furnacalis) on the intercropping corn plants decreased by based on the average of seven surveys per year for each treatment 2.9 to 17 heads per 30 plants compared with that on the monoculture corn plants. The number of natural enemy insect species on corn plants under intercropping was significantly higher than that under corn monoculture. That is, intercropping may decrease the population of Asian corn borers by increasing S, H, E, and natural enemy insect species (NEI). Moreover, intercropping type and fertilizer level significantly affected corn leaf nutrient contents. Compared with the normal fertilizer level, fertilizer reduction significantly reduced the foliar contents of amino acids, soluble protein, and soluble sugar in corn plants. In addition, corn-soybean and corn-peanut intercropping significantly increased the three nutrient contents in corn leaves compared with corn monoculture. In terms of corn nutrients, intercropping could compensate for the effects of fertilizer reduction. The foliar content of JA in corn-soybean intercropping was significantly higher than in corn monoculture. Under corn-soybean and corn-peanut intercropping, SA was significantly lower than under corn monoculture. Overall, intercropping, not fertilizer reduction, can significantly increase insect community diversity while reducing the population abundances of the key insect pest species on corn plants. Intercropping reduced the SA content, increased amino acids and thus reduced the susceptibility of corn to the pest insects.

[Spatial Distribution of Quinolone Antibiotics and Its Correlation Relationship with Microbial Community in Soil of Shijiazhuang City]

Microbial communities are an important component of soil ecosystems. Long-term low content antibiotic pollution will affect the structure and function of microbial communities in soil. Therefore, Shijiazhuang City was selected as the study area, in which twelve sample points were set up in September 2020. These sample sites were divided into four areas (S1, S2, S3, and S4) according to spatial orientation. Ultra-high performance liquid chromatography-mass spectrometry (HPLC-MS/MS) was applied to determine the content of typical antibiotic-quinolones (QNs) in the soil. 16S rRNA high-throughput sequencing technology was used to study the microbial community structure and diversity in the soil. The results showed that:① the total detected contents of QNs in the four areas were S3 (313.5 μg·kg^-1)>S4 (65.54 μg·kg^-1)>S1 (46.19 μg·kg^-1)>S2 (12.63 μg·kg^-1). The content of norfloxacin (NOR) was the highest (91.99 μg·kg^-1), whereas the content of oxolinic acid (OXO) was the lowest (0.4486 μg·kg^-1). ② For grain size, the proportion of powder (2-50 μm) was the highest (66.7%-93.2%), whereas the proportion of clay (less than 2 μm) was the lowest (2.50%-9.10%). For physical and chemical parameters, total phosphorus (TP) and ammonia nitrogen (NH₄⁺-N) showed non-significant spatial differences, whereas nitrate nitrogen (NO₃^--N), nitrite nitrogen (NO₂^--N), and grain size showed significant spatial differences. ③ For microbial community composition, there were six dominant bacteria phyla and five dominant bacteria genera, among which Actinobacteriota (18.3%-34.6%) and Proteobacteria (13.6%-34.1%) were the dominant bacteria phyla, and Arthrobacter (3.24%-8.61%) and Nitrososphaeraceae (2.93%-9.46%) were the dominant bacteria genera. The diversity results showed the highest value in the S2 area (6.48) and the lowest value in the S3 area (5.89). ④ QNs and soil physical and chemical parameters significantly changed the structural composition of microbial communities, and OXO, NO₃^--N, and soil particle size affected the diversity of microbial communities. FLU, NH₄⁺-N, NO₂^--N, and soil particle size affected the function of the microbial community. Therefore, it is necessary to further strengthen the risk control of antibiotics in the soil of Shijiazhuang City.

Community diversity determines the evolution of synthetic bacterial communities under artificial selection

Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function. Working with communities instead of individuals as selection units brings in additional sources of variation in the considered function that can influence the outcome of the artificial selection. In this study, we wanted to assess the effect of manipulating the initial community richness on artificial selection efficiency, defined as the change in the targeted function over time. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their richness (from one to 16 strains). Overall, the selected communities were 16% more productive than the control communities, but a convergence of community composition might have limited the effect of diversity on artificial selection efficiency. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. We propose that applying artificial selection on communities varying for their diversity could be a way to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.

[Differences in Bacterial Community Structure in Rhizosphere Soil of Three Caragana Species and Its Driving Factors in a Common Garden Experiment]

The soil bacterial diversity and community structures in rhizosphere soil of Caragana microphylla, Caragana liouana, and Caragana roborovskyi in a common garden experiment were measured using the high-throughput sequencing technique, with the aim of investigating the factors driving the variation in the bacterial community structure. The results indicated that 42 phyla, 55 classes, 123 orders, 244 families, and 558 genera were obtained from the rhizosphere soil. The dominant phyla in all sample sites were Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Acidobacteria (relative abundance>1%). At the genus level, Phenylobacterium, Ensifer, and Chitinophaga were dominant. Two-way analysis of variance showed that species had a significant effect on the Shannon index and Simpson index of rhizosphere soil bacteria of the three Caragana species, whereas the Chao1 index, Shannon index, and Simpson index were significantly affected by the interaction of provenances and species. There was a significant difference among the three species in the composition of bacterial communities, and the cluster analysis indicated that the composition of the soil bacterial community significantly differed among provenances in C. liouana and C. roborovskyi. Based on the redundancy analysis, mean annual precipitation and altitude were the dominant factors influencing the rhizosphere soil bacterial community structure. Overall, the present results indicated that there were intraspecific and interspecific differences in the diversity and community structures of rhizosphere soil bacteria, and the bacterial community structure was mainly affected by the provenance climate. These results provide a theoretical basis for understanding the adaptation strategies and ecological restoration of the three Caragana species.

Effects of Grass Inter-Planting on Soil Nutrients, Enzyme Activity, and Bacterial Community Diversity in an Apple Orchard

The orchard inter-planting pattern is being widely used in many countries of the world, but it is relatively new in China. This study evaluated the interrow mono- and mixed-planting of Lolium perenne (Lp) and Medicago sativa (Ms) in orchards on soil nutrient, enzyme activity, and bacterial community diversity in 0-10, 10-20, and 20-40 cm soil layers. The clean tillage orchard was used as control (CK) treatment. Compared with CK, Lp and Lp + Ms. significantly increased the contents of soil organic matter (OM), total nitrogen (TN), and alkali-hydrolyzable nitrogen (AN) in 0-20-cm soil layer, and up-regulated the activities of urease (URE) and alkaline phosphatase (ALP). The Lp treatment significantly increased the relative abundance of Gemmatimonadetes and Planctomycetes in the 0-10-cm soil layer. Besides, cover crops significantly increased the abundance of Actinobacteria, Gemmatimonadetes, and Chloroflexi in the 10-20-cm soil layer and that of Gemmatimonadetes and Chloroflexi in the 20-40 cm soil layer. The redundancy analysis (RDA) showed significant positive correlations of Actinobacteria with ALP, OM and TN and that of Bacteroidetes with available potassium (AK), and Proteobacteria with available phosphorus (AP). Overall, the grass inter-planting improved the soil nutrients, enzymes activities, and bacterial community composition of the soil. Based on these results, inter-planting perennial ryegrass in the apple orchards is a suitable grass-orchard inter-planting strategy in Weibei, Shaanxi Province of China.

[Structure and Functional Diversity of Bacterial Community in Rhizosphere Soil of Typical Vegetation in the Riparian Zone Along the Downstream of Songhua River]

The aim of this study was to provide a reference for the riparian zone with protection and ecological restoration by analyzing the differences in typical vegetation (Phragmites communis, Populus tomentosa, Salix sungkianica, and Carex schmidtii) rhizosphere bacterial communities and their functions and identifying the potential of different types of vegetation to restore the damaged riparian zone in Songhua River. The 16S rRNA of rhizosphere soil bacteria in the four typical vegetation types of the riparian zone along the downstream of the Songhua River was sequenced using the Illumina MiSeq PE300 high-throughput sequencing platform. The community diversity, functional differences, and influencing factors of rhizosphere soil bacteria for different vegetation types were analyzed. The results showed that the Ace index, Chao1 index, and Shannon index of soil bacterial diversity in P.communis were significantly higher than those of P.tomentosa (P<0.05), and there was no significant difference between the above two types of vegetation and S. sungkianica and C.schmidtii. There were significant differences between the soil bacterial community structure of P. tomentosa and that of the three other vegetation types (P<0.05). The soil bacterial community structures of S.sungkianica, C.schmidtii, and P.communis were similar. Bacteria in the rhizosphere soil of the four typical vegetation types could be divided into 38 phyla. Acidobacteria, Actinobacteria, Chloroflexi, Verrucomicrobia, and Proteobacteria were the dominant phyla (relative abundance>5%), and the Nitrospirae, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Rokubacteria of bacteria had a relative abundance greater than 1%. The bacterial community in the rhizosphere soil of the four typical vegetation types had 6 primary metabolic pathways and 43 secondary metabolic pathways, including 14 types of main secondary metabolic pathways (relative abundance>1%). Diversity in rhizosphere soil bacterial communities of different vegetation types was significantly influenced by the C/N ratio, soil pH, and moisture content. Hence, the effects of different vegetation types in repairing the degraded riparian zone were different, and wetland vegetation (S.sungkianica and C.schmidtii) was conducive to the improvement in soil bacterial diversity and soil ecosystem functions.

[Effect of Different Land Use Types on the Diversity of Soil Bacterial Community in the Coastal Zone of Jialing River]

The purpose of this study was to clarify the differences in soil bacterial community diversity in different land uses in the coastal zone of the Jialing River and to provide theoretical reference for reasonable land development and resource protection of the Jialing River basin. Based on second generation high-throughput sequencing technology, the diversity, structural composition, functional types, and influencing factors of soil bacterial communities in different land use types were analyzed. The results showed that:① there were some differences in soil physical and chemical properties among different land uses. The nutritional indexes of agricultural land and soil wetland were significantly higher than those of natural forest land and sandy soil wetland (P<0.05). ②The Ace, Shannon, and Chao indexes of sandy soil wetland and soil wetland were significantly higher than those of natural forest land and agricultural land (P<0.05). The Simpson index of soil bacteria in different land use types was significantly different (P<0.05). ③ The dominant phyla of soil bacteria in the coastal zone of the Jialing River were Proteobacteria, Actinobacteriata, Acidobacteriata, and Chloroflexi, and the relative abundance accounted for more than 65%. The community structure of sandy soil wetland was similar to that of soil wetland and was significantly different from that of other land use types (P<0.05). ④ Primary functional metabolism was the core function of the bacterial community, accounting for more than 75%. Agricultural activities had the greatest impact on the community function, which significantly improved the metabolism of amino acids and carbohydrates, enhanced the utilization of nitrogen and phosphorus, reduced the metabolism of energy and coenzyme vitamins, and weakened the resistance of bacterial community to environmental impact (P<0.05). ⑤ Total phosphorus (TP) was the key influencing factor of the soil bacterial community. In conclusion, the construction of the wetland habitat in the Jialing River coastal zone is most conducive to the development of underground ecological diversity and the stability of the soil ecosystem.

Interaction capacity as a potential driver of community diversity

How patterns in community diversity emerge is a long-standing question in ecology. Studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here, I analysed time-varying interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modelling, and introduced 'interaction capacity', namely, the sum of interaction strength that a single species gives and receives, as a potential driver of community diversity. As community diversity increases, the number of interactions increases exponentially but the mean interaction capacity of a community becomes saturated, weakening interspecific interactions. These patterns are modelled with simple mathematical equations, based on which I propose the 'interaction capacity hypothesis': that interaction capacity and network connectance can be two fundamental properties that influence community diversity. Furthermore, I show that total DNA abundance and temperature influence interaction capacity and connectance nonlinearly, explaining a large proportion of diversity patterns observed in various systems. The interaction capacity hypothesis enables mechanistic explanations of community diversity. Therefore, analysing ecological community data from the viewpoint of interaction capacity would provide new insight into community diversity.

30 Years of postdisturbance recruitment in a Neotropical forest

QUESTIONS

Long-term community response to disturbance can follow manifold successional pathways depending on the interplay between various recruitment processes. Analyzing the succession of recruited communities provides a long-term perspective on forest response to disturbance. Specifically, postdisturbance recruitment trajectories assess (a) the successive phases of postdisturbance response and the role of deterministic recruitment processes, and (b) the return to predisturbance state of recruits taxonomic/functional diversity/composition.

LOCATION

Amazonian rainforest, Paracou station, French Guiana.

METHODS

We analyzed trajectories of recruited tree communities, from twelve forest plots of 6.25 ha each, during 30 years following a disturbance gradient that ranged from 10% to 60% of aboveground biomass removed. We measured recruited community taxonomic composition turnover, compared to whole predisturbance community, and assessed their functional composition by measuring the community weighted means for seven leaf, stem, and life-history functional traits. We also measured recruited community taxonomic richness, taxonomic evenness, and functional diversity and compared them to the diversity values from a random recruitment process.

RESULTS

While control plots trajectories resembled random recruitment trajectories, postdisturbance trajectories diverged significantly. This divergence corresponded to an enhanced recruitment of light-demanding species that became dominant above a disturbance intensity threshold. After breakpoints in time, though, recruitment trajectories returned to diversity values and composition similar to those of predisturbance and control plots community.

CONCLUSIONS

Following disturbance, recruitment processes specific to undisturbed community were first replaced by the emergence of more restricted, deterministic recruitment processes favoring species with efficient light use and acquisition. Then, a second phase corresponded to a decades-long recovery of recruits predisturbance taxonomic and functional diversity and composition that remained unachieved after 30 years.

A High Rate Algal Pond Hosting a Dynamic Community of RNA Viruses

Despite a surge of RNA virome sequencing in recent years, there are still many RNA viruses to uncover-as indicated by the relevance of viral dark matter to RNA virome studies (i.e., putative viruses that do not match to taxonomically identified viruses). This study explores a unique site, a high-rate algal pond (HRAP), for culturing industrially microalgae, to elucidate new RNA viruses. The importance of viral-host interactions in aquatic systems are well documented, and the ever-expanding microalgae industry is no exception. As the industry becomes a more important source of sustainable plastic manufacturing, a producer of cosmetic pigments and alternative protein sources, and a means of CO2 remediation in the face of climate change, studying microalgal viruses becomes a vital practice for proactive management of microalgae cultures at the industrial level. This study provides evidence of RNA microalgal viruses persisting in a CO2 remediation pilot project HRAP and uncovers the diversity of the RNA virosphere contained within it. Evidence shows that family Marnaviridae is cultured in the basin, alongside other potential microalgal infecting viruses (e.g., family Narnaviridae, family Totitiviridae, and family Yueviridae). Finally, we demonstrate that the RNA viral diversity of the HRAP is temporally dynamic across two successive culturing seasons.

Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust

Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.

Characteristics and metabolic patterns of soil methanogenic archaea communities in the high-latitude natural forested wetlands of China

Soil methanogenic microorganisms are one of the primary methane-producing microbes in wetlands. However, we still poorly understand the community characteristic and metabolic patterns of these microorganisms according to vegetation type and seasonal changes. Therefore, to better elucidate the effects of the vegetation type and seasonal factors on the methanogenic community structure and metabolic patterns, we detected the characteristics of the soil methanogenic mcrA gene from three types of natural wetlands in different seasons in the Xiaoxing'an Mountain region, China. The results indicated that the distribution of Methanobacteriaceae (hydrogenotrophic methanogens) was higher in winter, while Methanosarcinaceae and Methanosaetaceae accounted for a higher proportion in summer. Hydrogenotrophic methanogenesis was the dominant trophic pattern in each wetland. The results of principal coordinate analysis and cluster analysis showed that the vegetation type considerably influenced the methanogenic community composition. The methanogenic community structure in the Betula platyphylla-Larix gmelinii wetland was relatively different from the structure of the other two wetland types. Indicator species analysis further demonstrated that the corresponding species of indicator operational taxonomic units from the Alnus sibirica wetland and the Betula ovalifolia wetland were similar. Network analysis showed that cooperative and competitive relationships exist both within and between the same or different trophic methanogens. The core methanogens with higher abundance in each wetland were conducive to the adaptation to environmental disturbances. This information is crucial for the assessment of metabolic patterns of soil methanogenic archaea and future fluxes in the wetlands of the Xiaoxing'an Mountain region given their vulnerability.

Endophytic Fungal Community of Tobacco Leaves and Their Potential Role in the Formation of "Cherry-Red" Tobacco

"Cherry-red" tobacco is the superior variant of tobacco, appearing with the apperance of red dapples on cured leaves due to the demethylation of nicotine to nornicotine during maturation and curing. Fungi are known to have the capacity to convert nicotine to nornicotine. However, an endophytic fungal community of "cherry-red" tobacco has never been reported to our best knowledge. Here, we sampled mature leaves from both "cherry-red" and ordinary tobacco at lower, center, and upper plant sections, and we analyzed the ITS diversity using high-throughput sequencing. Results revealed a significantly different fungal community of foliar endophyte in "cherry-red" and ordinary tobacco. In comparison to the ordinary control, higher diversity and a co-occurrence network complex were found in "cherry-red" samples, especially in the center and upper leaves, where the red dapples mainly emerged. More taxa were enriched in the "cherry-red" than ordinary tobacco leaves at all plant sections. In particular, Aspergillus, some strains of which are reported capable of converting nicotine to nornicotine, was specifically enriched in upper "cherry-red" tobacco leaves, which showed most red dapples after curing. A less robust network structure was detected in the "cherry-red" tobacco compared to ordinary tobacco. The nearest taxon index (NTI) and β NTI indicated that the local community structuration of tobacco endophytic fungi mainly driven by deterministic process, while the community turnover among plant sections was stochastic. In conclusion, our study provides the earliest information of endophytic fungal community in "cherry-red" tobacco leaf, and the community diversity, composition, and network features are synchronously varied with the appearance of red dapples, which is suggestive of their relationship to the formation of "cherry-red" tobacco.

Molecular Microbial Community Analysis as an Analysis Tool for Optimal Biogas Production

The microbial diversity in anaerobic digestion (AD) is important because it affects process robustness. High-throughput sequencing offers high-resolution data regarding the microbial diversity and robustness of biological systems including AD; however, to understand the dynamics of microbial processes, knowing the microbial diversity is not adequate alone. Advanced meta-omic techniques have been established to determine the activity and interactions among organisms in biological processes like AD. Results of these methods can be used to identify biomarkers for AD states. This can aid a better understanding of system dynamics and be applied to producing comprehensive models for AD. The paper provides valuable knowledge regarding the possibility of integration of molecular methods in AD. Although meta-genomic methods are not suitable for on-line use due to long operating time and high costs, they provide extensive insight into the microbial phylogeny in AD. Meta-proteomics can also be explored in the demonstration projects for failure prediction. However, for these methods to be fully realised in AD, a biomarker database needs to be developed.

The characteristics of soil fungal community in degraded alpine meadow in the Three Rivers Source Region, China

To clarify the variation of species composition, diversity, and functional structure of soil fungi community along alpine meadow degradation,we examined the characteristics and controlling factors of soil fungal communities in non-degraded, lightly degraded, moderately degraded, severely degraded and extremely degraded (black soil beach) alpine meadows at the Three Rivers Source Region, based on the high-throughput gene sequencing and FUNGuild functional prediction. The results showed that the dominant phyla in alpine meadow soil were Ascomycota, Basidiomycetes, and Mortierellomycota. Species composition of soil fungal community varied greatly in alpine meadow under different levels of degradation. The abundance of Cladosporium flabelliforme, Entoloma sodale, Hygrocybe conica, Inocybe sp. and Trichocladium opacum increased, while that of Gibberella tricincta and Dactylonectria macrodidyma decreased following grassland degradation. The meadow under severe degradation had higher soil fungal Chao1 index, while that under light degradation had lower Shannon index and Simpson index. The abundance of pathologic, symbiotic, and saprophytic types of fungi varied among different alpine meadows. Along with the grassland degradation, the abundance of soil symbiotic fungi decreased, while that of pathological fungi increased. The soil fungal community and functional compositions changed obviously with degradation in the alpine meadow. Plant aboveground biomass, soil water content, pH, total organic carbon, total nitrogen, ammonium nitrogen, available phosphate, total potassium and AN/AP (ratio of available nitrogen and available phosphorus) were the main driving factors for the variations in soil fungal community structure.

Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake

Large amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes' effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.

[Effects of Land Use Changes on Soil Bacterial Community Diversity in the Riparian Wetland Along the Downstream of Songhua River]

The aim of this study was to provide a theoretical basis for the restoration of degraded wetlands in the Songhua River by determining the effect of habitat quality changes on the soil bacterial community. The 16S rDNA of soil bacteria in five land use types (natural wetland, paddy field, corn field, sand mining slash, restoration wetland) of the riparian wetland along the downstream of the Songhua River was sequenced using the Illumina MiSeq PE300 high-throughput sequencing platform. The differences in the community diversity and functions of soil bacteria for different land use types were analyzed. ACE, Chao1, and Shannon indices of soil bacterial diversity were significantly reduced by reclaiming the wetland into the corn field (P<0.05), and they were significantly improved by wetland restoration in the sand mining slash (P<0.05). The differences in the soil bacterial community structure were significant among natural wetlands, paddy fields, corn fields, and sand mines (P<0.05). Similar bacterial community structures were found in sand mining slash and restoration wetlands. Soil bacteria in the riparian wetland can be divided into 40 phyla, 105 classes, 258 orders, 421 families, 802 genera, and 1673 species. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, Firmicutes, and Gemmatimonadetes were the dominant phyla (relative abundance>1%). In contrast, Bacteroidetes preferred the soil under the paddy environment, Proteobacteria and Gemmatimonadales preferred the soil environment of corn, and Actinobacteria preferred the soil environment of sand mining slash. Wetland soil bacteria have six primary metabolic pathways (metabolism, environmental information processing, genetic information processing, cellular processes, human disease, and organismal systems) and 46 secondary metabolic pathways including 19 types of main secondary metabolic pathways (relative abundance>1%). Diversity of the soil fungal community was significantly influenced by soil pH, moisture content, available nitrogen, and the C/N ratio. Hence, potential ecological risks increased and ecosystem stability decreased because of the resource development activities in natural wetlands. Diversity of the soil fungal community plays a critical role in protecting the ecological security and supplying considerable amounts of undeveloped resources.

The effect of sulfamonomethoxine treatment on the gut microbiota of Nile tilapia (Oreochromis niloticus)

To investigate the possible effects of sulfamonomethoxine (SMM) on Nile tilapia (Oreochromis niloticus), we quantitatively evaluated the microbial shifts in the intestines of Nile tilapia in response to different doses of SMM (200 and 300 mg/kg) using 16S rRNA gene sequencing. At the phylum level, the control group (0 mg kg^-1  SMM) was dominated by Actinobacteria, Proteobacteria, and Firmicutes. In the treatment groups, Firmicutes, Proteobacteria, and Chloroflexi were the dominant phyla. Cluster analysis indicated that the two groups treated with SMM clustered together. Similarly, the bacterial families that dominated the control group differed from those dominating the treatment groups. The changes in intestinal microbial composition over time were similar between the two SMM treatment groups. In both groups, the abundances of some families, including the Bacillaceae, Streptococcaceae, and Pseudomonadaceae, increased first and then decreased. Overall, the addition of SMM to the feed changed the structure of the intestinal microbiota in Nile tilapia. This study improves our understanding of the impact of SMM on the intestinal microenvironment of Nile tilapia. Our results provide guidelines for the feasibility of SMM use in aquaculture production.

Community diversity outweighs effect of warming on plant colonization

Abiotic environmental change, local species extinctions and colonization of new species often co-occur. Whether species colonization is driven by changes in abiotic conditions or reduced biotic resistance will affect community functional composition and ecosystem management. We use a grassland experiment to disentangle effects of climate warming and community diversity on plant species colonization. Community diversity had dramatic impacts on the biomass, richness and traits of plant colonists. Three times as many species colonized the monocultures than the high diversity 17 species communities (~30 vs. 10 species), and colonists collectively produced 10 times as much biomass in the monocultures than the high diversity communities (~30 vs. 3 g/m² ). Colonists with resource-acquisitive strategies (high specific leaf area, light seeds, short heights) accrued more biomass in low diversity communities, whereas species with conservative strategies accrued most biomass in high diversity communities. Communities with higher biomass of resident C4 grasses were more resistant to colonization by legume, nonlegume forb and C3 grass colonists, but not by C4 grass colonists. Compared with effects of diversity, 6 years of 3°C-above-ambient temperatures had little impact on plant colonization. Warmed subplots had ~3 fewer colonist species than ambient subplots and selected for heavier seeded colonists. They also showed diversity-dependent changes in biomass of C3 grass colonists, which decreased under low diversity and increased under high diversity. Our findings suggest that species colonization is more strongly affected by biotic resistance from residents than 3°C of climate warming. If these results were extended to invasive species management, preserving community diversity should help limit plant invasion, even under climate warming.

[Spatio-temporal Patterns of Microbial Communities and Their Driving Mechanisms in Subalpine Lakes, Ningwu, Shanxi]

Human activities and climate change cause the degradation of subalpine lake ecosystems, which induce the shift of microbial community structure. The spatio-temporal dynamics and the diversity maintenance mechanisms of bacterial communities in Gonghai Lake in Ningwu, Shanxi, were investigated by using Q-PCR and DGGE. The results showed that the temperature), pH, dissolved oxygen, electrical conductivity salinity, and ammonium nitrogen (NH₄⁺) contestation were significantly different among the different sampling depths during different months. Bacterial abundance was the highest in August and the lowest in November, and the abundance was higher in the middle water layer (2 m, 4 m, and 6 m depths), but relatively low in the surface layer and bottom layer (0 m and 8 m depths, respectively). The α diversity index of bacterial communities had significant differences among the different months and depths, and showed an initial decreasing trend and then an increasing trend from April to December. A PERMANOVA test showed that the spatial distribution of bacterial communities was significantly different among depths (P<0.001). The results of redundancy analysis and variation partitioning indicated that environmental selection and diffusion limitation had an effect on the maintenance of the diversity patterns of bacterial communities at the different depths of GH. However, the relative effect of environmental factors was stronger, of which the concentration of NO₃^-, NO₂^-, and NH₄⁺ were the main influencing factors. In conclusion, the bacterial communities in GH subalpine lake showed clear spatio-temporal distribution patterns, and environmental variables had a significant effect on shaping the community diversity.

The alterations of gut microbiota in mice with chronic pancreatitis

Background

The changes of intestinal microbiome are associated with inflammatory, metabolic, and malignant disorders, and there are no studies assessing the intestinal microbiota of mice with chronic pancreatitis (CP). Thus, we aim to investigate the variations in diversity, composition and function of intestinal microbiota in CP mice.

Methods

Sixteen male C57BL/6 mice were randomly selected, and divided into two groups, treated intraperitoneally with saline (normal control group, CT group) or ethanol + cerulein (experimental group, CP group) for 6 weeks. Body weight as measured in entire processes. Histopathological examination of CP index was conducted to verify the CP induction. Extracted DNA from colon samples was used for Illumina HiSeq sequencing of the bacterial V4 region of 16S rRNA gene and analyzed using Quantitative Insights Into Microbial Ecology (QIIME). Functional profiling of microbial communities was predicted with BugBase.

Results

Significant alterations of the gut microbiota were found in the CP mice compared to CT groups, as revealed by significant decrease in bacterial richness and diversity, declined the relative abundance of Lachnospiraceae_NK4A136, Ruminiclostridium and Roseburia, and increased the relative abundances of Bacteroides and Alloprevotella genera. Analysis of microbial community-level phenotypes revealed significant differences in nine phenotypes (aerobic, anaerobic, containing mobile elements, facultatively anaerobic, biofilm forming, gram-negative, gram-positive, potentially pathogenic, and stress tolerant) between CP group and CT group.

Conclusions

This study indicated that mice with CP had a distinct microbiota profile.

Aphids Influence Soil Fungal Communities in Conventional Agricultural Systems

Arbuscular mycorrhizal fungi (AMF) form symbioses with the roots of most plant species, including cereals. AMF can increase the uptake of nutrients including nitrogen (N) and phosphorus (P), and of silicon (Si) as well as increase host resistance to various stresses. Plants can simultaneously interact with above-ground insect herbivores such as aphids, which can alter the proportion of plant roots colonized by AMF. However, it is unknown if aphids impact the structure of AMF communities colonizing plants or the extent of the extraradical mycelium produced in the soil, both of which can influence the defensive and nutritional benefit a plant derives from the symbiosis. This study investigated the effect of aphids on the plant-AMF interaction in a conventionally managed agricultural system. As plants also interact with other soil fungi, the non-AMF fungal community was also investigated. We hypothesized that aphids would depress plant growth, and reduce intraradical AMF colonization, soil fungal hyphal density and the diversity of AM and non-AM fungal communities. To test the effects of aphids, field plots of barley enclosed with insect proof cages were inoculated with Sitobion avenae or remained uninoculated. AMF specific and total fungal amplicon sequencing assessed root fungal communities 46 days after aphid addition. Aphids did not impact above-ground plant biomass, but did increase the grain N:P ratio. Whilst aphid presence had no impact on AMF intraradical colonization, soil fungal hyphal length density, or AMF community characteristics, there was a trend for the aphid treatment to increase vesicle numbers and the relative abundance of the AMF family Gigasporaceae. Contrary to expectations, the aphid treatment also increased the evenness of the total fungal community. This suggests that aphids can influence soil communities in conventional arable systems, a result that could have implications for multitrophic feedback loops between crop pests and soil organisms across the above-below-ground interface.

Salinity Is a Key Determinant for Soil Microbial Communities in a Desert Ecosystem

Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.

Soil salinization is a growing environmental problem caused by both natural and human activities. Excessive salinity in soil suppresses growth, decreases species diversity, and alters the community composition of plants; however, the effect of salinity on soil microbial communities is poorly understood. Here, we characterize the soil microbial community along a natural salinity gradient in Gurbantunggut Desert, Northwestern China. Microbial diversity linearly decreased with increases in salinity, and community dissimilarity significantly increased with salinity differences. Soil salinity showed a strong effect on microbial community dissimilarity, even after controlling for the effects of spatial distance and other environmental variables. Microbial phylotypes (n = 270) belonging to Halobacteria, Nitriliruptoria, [Rhodothermi], Gammaproteobacteria, and Alphaproteobacteria showed a high-salinity niche preference. Out of nine potential phenotypes predicted by BugBase, oxygen-related phenotypes showed a significant relationship with salinity content. To explore the community assembly processes, we used null models of within-community (nearest-taxon index [NTI]) and between-community (βNTI) phylogenetic composition. NTI showed a significantly negative relationship with salinity, suggesting that the microbial community was less phylogenetically clustered in more-saline soils. βNTI, the between-community analogue of NTI, showed that deterministic processes have overtaken stochastic processes across all sites, suggesting the importance of environmental filtering in microbial community assembly. Taken together, these results suggest the importance of salinity in soil microbial community composition and assembly processes in a desert ecosystem.

IMPORTANCE Belowground microorganisms are indispensable components for nutrient cycling in desert ecosystems, and understanding how they respond to increased salinity is essential for managing and ameliorating salinization. Our sequence-based data revealed that microbial diversity decreased with increasing salinity, and certain salt-tolerant phylotypes and phenotypes showed a positive relationship with salinity. Using a null modeling approach to estimate microbial community assembly processes along a salinity gradient, we found that salinity imposed a strong selection pressure on the microbial community, which resulted in a dominance of deterministic processes. Studying microbial diversity and community assembly processes along salinity gradients is essential in understanding the fundamental ecological processes in desert ecosystems affected by salinization.

[Analysis of the Temporal and Spatial Distribution of the Diversity of the Denitrifying Anaerobic Methane-Oxidizing Bacterial Community in the Sediments of the Hunhe River and Its Relationship with Environmental Factors]

16S rRNA and pmoA functional genes were used as biomarker genes to investigate the temporal and spatial distribution of community diversity of Candidatus Methylomirabilis oxyfera (M. oxyfera) in the sediments of the Hunhe River by clone library technology. The dependence relationship between the physicochemical property of water and sediment samples and the diversity characteristics of the M. oxyfera community were analyzed by multivariate direct gradient analysis. Among the examples collected in September 2014, the OTU number of the 16S rRNA gene of M. oxyfera was 2-5, the Shannon-Wiener diversity index was 0.21-1.4, and the distribution characteristics in the middle reaches > upstream > downstream were presented. The OTU number and Shannon-Wiener diversity index of the pmoA functional gene in upstream samples are significantly higher than those in the middle and lower reach samples, and the Shannon-Wiener diversity indices in the upstream samples are 3.5 times and 2.3 times higher than that of the middle and the downstream samples, respectively. The community diversity of M. oxyfera showed a distinct regional distribution. Samples were collected at 3 sampling points in March 2015. The OTU values of 16S rRNA and pmoA for M. oxyfera are 6 and 5 respectively, which were obviously higher than those in September 2014. The Shannon-Wiener index is also higher than that in September 2014 (1.4>0.68; 57>0.00). The community diversity of M. oxyfera showed obvious seasonal distribution characteristics. Multivariate direct gradient analysis results showed that the concentration of DOC in water, sediment conductivity, TOC concentration, and nitrite concentration in the sediment are the main environmental factors affecting the community diversity of M. oxyfera.

[Community structure of soil mites under Quercus variabilis forests in small watershed of karst area, Guizhou, China.]

To analyze the differences of community structure of soil mites between the rocky desertification environment and karst beech forests, we investigated the soil mites of Quercus variabilis forest in the Chaoying small watershed of Guizhou Province. Soil mites from 83 genera, 54 families, and 3 orders were collected in the four investigations of 2014. We analyzed the differences of genus numbers, individual numbers, individual density, Shannon diversity index (H), Margalef richness index (SR), Pielou evenness index (J), maturity index (MI) of predatory soil mites (Mesostigmata: Gamasina), community structure of the oribatid mites (MGP) and nutritional structure of mite. Results showed that Oribatida was dominant in taxonomic richness and individual abundance. Abundant genus, high individual density and diversity of soil mites were found in summer and autumn, and higher individual abundance was found in spring and autumn. Soil mites showed surface-aggregation in their distribution. Most predatory mites were K-selected in summer and r-selected in other seasons. The ecological groups of the oribatid mites were mainly P-type and O-type. Hypochthonius, Allobelba and Zygoribatula constituted the nutrient function group of the soil mites. There were significant differences in the main groups of soil mites in the beech forest and other forest types. Among all the groups, Parholaspididae, Laelapidae, Oppiidae and Haplozetidae with abundant genera composition, Multioppia, Parholaspulus, Scheloribates and Haplozetes with predominance could be used as a biological indicator for the soil environment in beech forests.

Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut

Many factors shape the ability of different microbes to coexist in microbial communities. In the human gut, dietary and host-derived nutrients largely drive microbial community structure. How gut microbes with very similar nutrient profiles are able to coexist over time within the same host is not fully understood. Tuncil et al. (mBio 8:e01068-17, 2017, https://doi.org/10.1128/mBio.01068-17) explored glycan prioritization in two closely related human gut bacteria, Bacteroides ovatus and Bacteroides thetaiotaomicron, on complex glycan mixtures that both organisms can degrade. Determining depletion of the individual glycans over time in pure cultures and cocultures revealed that the bacteria seem to have hardwired differences in their preferences for different glycans which likely contribute to their stable coexistence. The researchers also established that gene expression changes of the corresponding polysaccharide utilization loci did not always mirror glycan depletion, which highlights that additional regulatory mechanisms must be present.

Shift in community structure in an early-successional Mediterranean shrubland driven by long-term experimental warming and drought and natural extreme droughts

Global warming and recurring drought are expected to accelerate water limitation for plant communities in semiarid Mediterranean ecosystems and produce directional shifts in structure and composition that are not easily detected, and supporting evidence is scarce. We conducted a long-term (17 years) nocturnal-warming (+0.6°C) and drought (-40% rainfall) experiments in an early-successional Mediterranean shrubland to study the changes in community structure and composition, contrasting functional groups and dominant species, and the superimposed effects of natural extreme drought. Species richness decreased in both the warming and drought treatments. Responses to the moderate warming were associated with decreases in herb abundance, and responses to the drought were associated with decreases in both herb and shrub abundances. The drought also significantly decreased community diversity and evenness. Changes in abundance differed between herbs (decreases) and shrubs (increases or no changes). Both warming and drought, especially drought, increased the relative species richness and abundance of shrubs, favoring the establishment of shrubs. Both warming and drought produced significant shifts in plant community composition. Experimental warming shifted the community composition from Erica multiflora toward Rosmarinus officinalis, and drought consistently shifted the composition toward Globularia alypum. The responses in biodiversity (e.g., community biodiversity, changes of functional groups and compositional shifts) were also strongly correlated with atmospheric drought (SPEI) in winter-spring and/or summer, indicating sensitivity to water limitation in this early-successional Mediterranean ecosystem, especially to natural extreme droughts. Our results suggest that the shifts in species assembles and community diversity and composition are accelerated by the long-term nocturnal-warming and drought, combined with natural severe droughts, and that the magnitude of the impacts of climate change is also correlated with the successional status of ecosystem. The results thus highlight the necessity for assessing the impacts on ecosystemic functioning and services and developing effective measures for conserving biodiversity.

Functional traits explain ecosystem function through opposing mechanisms

The ability to explain why multispecies assemblages produce greater biomass compared to monocultures, has been a central goal in the quest to understand biodiversity effects on ecosystem function. Species contributions to ecosystem function can be driven by two processes: niche complementarity and a selection effect that is influenced by fitness (competitive) differences, and both can be approximated with measures of species' traits. It has been hypothesised that fitness differences are associated with few, singular traits while complementarity requires multidimensional trait measures. Here, using experimental data from plant assemblages, I show that the selection effect was strongest when trait dissimilarity was low, while complementarity was greatest with high trait dissimilarity. Selection effects were best explained by a single trait, plant height. Complementarity was correlated with dissimilarity across multiple traits, representing above and below ground processes. By identifying the relevant traits linked to ecosystem function, we obtain the ability to predict combinations of species that will maximise ecosystem function.

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing

The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.

Recent changes in mountain grasslands: a vegetation resampling study

Understanding how land-use changes affect different facets of plant biodiversity in seminatural European grasslands is of particular importance for biodiversity conservation. As conclusions of previous experimental or synchronic observational studies did not converge toward a general agreement, assessing the recent trends in vegetation change in various grassland systems using a diachronic approach is needed. In this resurvey study, we investigated the recent changes in grassland vegetation of the French Jura Mountains, a region with a long tradition of pastoralism. We compared the floristic composition of 150 grassland plots recorded between 1990 and 2000 with new relevés made in 2012 on the same plots. We considered taxonomic, phylogenetic and functional diversity as well as ecological characteristics of the plant communities derived from ecological indicator values and life strategies of the species. PCA of the floristic composition revealed a significant general trend linked to the sampling year. Wilcoxon paired tests showed that contemporary communities were generally more dominated by grass species and presented a higher tolerance to defoliation, a higher pastoral value, and a higher nutrient indicator value. Comparisons revealed a decrease in phylogenetic and functional diversity. By contrast, local species richness has slightly increased. The intensity of change in species composition, measured by Hellinger distance between pairs of relevés, was dependent on neither the time lag between the two surveys, the author of the first relevé nor its location or elevation. The most important changes were observed in grasslands that previously presented low pastoral value, low grass cover, low tolerance to defoliation, and high proportion of stress-tolerant species. This trend was likely linked to the intensification of grassland management reported in the region, with a parallel increase in mowing frequency, grazing pressure, and fertilization level. More restrictive specifications should be applied to agricultural practices to avoid overexploitation of mountain species-rich grasslands and its negative consequences on their biodiversity and resilience.

Biogeographic effects on early establishment of an invasive alien plant

PREMISE OF THE STUDY

Biotic resistance is often studied in the context of how interactions between native biota and invading species influence the success of those invaders. Seldom, however, is the strength of "resistance" compared biogeographically, where the ability of a species to impede invader establishment is contrasted between an invader's native and introduced recipient community.

METHODS

We conducted an experiment to examine how community diversity influences seedling recruitment of a plant invader where it is native and contrasted with results previously published from introduced ranges. In Switzerland, we created recipient communities that varied in species and functional richness and invaded them, or not, with seeds of Centaurea stoebe, a native European plant that has been previously used in an identical experiment in North America, where it is a prominent invader.

KEY RESULTS

The biogeographic comparison revealed that the recipient community largely prevented C. stoebe seedling establishment at home (Switzerland), but not away (Montana, USA), and that diversity of the resident vegetation did not contribute to the effects observed in the introduced range.

CONCLUSIONS

Our results provide evidence that differences in the biogeographic conditions and/or overall level of competition of resident community between the native and introduced range considerably suppresses seedling recruitment of the invasive plant, rather than resident diversity itself. In the case of C. stoebe, the surprisingly low establishment success in the experiments conducted in the native compared with the introduced range is likely to be influenced by the higher level of competition with resident community, by abiotic environmental conditions or interactions between these two factors in the native range. Release from factors suppressing seedling recruitment at home may contribute to the successful invasion of C. stoebe in North America.

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor

Aims

Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study.

Methods and Results

Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS.

Conclusions

Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species.

Significance and Impact of the Study

This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance.

Phylogenetic skew: an index of community diversity

The distribution of divergence times between member species of a community reflects the pattern of species composition. In this study, we contrast the species composition of a community against the meta-community, which we define as the species composition of a set of target communities. We regard the collection of species that comprise a community as a sample from the set of member species of the meta-community, and interpret the pattern of the community species composition in terms of the type of species sampled from the meta-community. A newly defined effective species sampling proportion explains the amount of the difference between the divergence time distributions of the community and that of the meta-community, assuming random sampling. We propose a new index of phylogenetic skew (PS), as the ratio of the maximum-likelihood estimate of the effective species sampling proportion to the observed sampling proportion. A PS value of 1 is interpreted as random sampling. If the value is >1, the sampling is suspected to be phylogenetically skewed. If it is <1, systematic thinning of species is likely. Unlike other indices, the PS does not depend on species richness as long as the community has more than a few members of a species. Because it is possible to compare partially observed communities, the index may be effectively used in exploratory analysis to detect candidate communities with unique species compositions from a large number of communities.

Host specialization in ticks and transmission of tick-borne diseases: a review

Determining patterns of host use, and the frequency at which these patterns change, are of key importance if we are to understand tick population dynamics, the evolution of tick biodiversity, and the circulation and evolution of associated pathogens. The question of whether ticks are typically host specialists or host generalists has been subject to much debate over the last half-century. Indeed, early research proposed that morphological diversity in ticks was linked to host specific adaptations and that most ticks were specialists. Later work disputed this idea and suggested that ticks are largely limited by biogeographic conditions and tend to use all locally available host species. The work presented in this review suggests that the actual answer likely lies somewhere between these two extremes. Although recent observational studies support the view that phylogenetically diverse host species share ticks when found on similar ecological ranges, theory on host range evolution predicts that host specialization should evolve in ticks given their life history characteristics. Contemporary work employing population genetic tools to examine host-associated population structure in several tick systems support this prediction and show that simple species records are not enough to determine whether a parasite is a true host generalist; host specialization does evolve in ticks at local scales, but may not always lead to speciation. Ticks therefore seem to follow a pattern of being global generalists, local specialists. Given this, the notion of host range needs to be modified from an evolutionary perspective, where one simply counts the number of hosts used across the geographic distribution, to a more ecological view, where one considers host use at a local scale, if we are to better understand the circulation of tick-borne pathogens and exposure risks for humans and livestock.

Surprisingly little population genetic structure in a fungus-associated beetle despite its exploitation of multiple hosts

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic structure in a beetle (Bolitotherus cornutus) that exploits three sympatric host fungi. We collected B. cornutus from plots containing the three host fungi in different proportions and quantified population genetic structure in each plot using a panel of microsatellite loci. We found no relationship between host community diversity and population differentiation in this species; however, we also found no evidence of resource-associated differentiation, suggesting that host fungi are not substantial barriers to gene flow. Moreover, we detected no genetic differentiation among B. cornutus populations separated by several kilometers, even though a previous study demonstrated moderate genetic structure on the scale of a few hundred meters. Although we found no effect of community diversity on population genetic structure in this study, the role of host communities in the structuring of genetic variation in heterogeneous landscapes should be further explored in a species that exhibits resource-associated population genetic structure.