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Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high‐throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia‐oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS‐type denitrifying community co‐varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities. Additionally, biotic interactions drove ammonia‐oxidizing and nirS‐type denitrifying communities by influencing species co‐occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N‐cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale. [ABSTRACT FROM AUTHOR]

Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22–56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments. [ABSTRACT FROM AUTHOR]

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section have long been overlooked. In this study, we performed a comprehensive investigation into the abundance, diversity and ecology of free-living (FL) and particle-associated (PA) microbial communities in seawater samples along the PN section during both summer and winter. Distinct hydrological conditions and resulting environmental gradients were observed between summer and winter, with clear features of intrusive Kuroshio subsurface water in summer and strong vertical mixing of seawater in winter. Bacterial abundance along the PN section was higher in summer (1.11  ×  108 copies·L−1 – 7.37  ×  108 copies·L−1) than in winter (1.83  ×  106 copies·L−1 – 1.34  ×  108 copies·L−1). Microbial diversity, as indicated by α-diversity indices, remained at relatively stable levels in summer, while a clear decreasing trend was observed in winter along the PN section. Additionally, the winter communities exhibited a more evident spatial shift along the PN section compared to the summer communities. 16S rRNA gene amplicon sequencing showed that microbial community composition varied considerably between different seasons (summer and winter) and lifestyles (FL and PA), with a notable dominance of Ralstonia species. in winter. Regarding the assembly of microbial communities, the stochastic process represented by dispersal limitation was the dominant process in summer, while the deterministic homogeneous selection was the most important process in winter. Correspondingly, distinct topological properties of the microbial co-occurrence networks were shown between different seasons and along the PN section. These results enhance our understanding of how hydrological conditions influence dynamic changes of microbial communities along the PN section, providing new insights for the microbial community assembly and interactions in such a complex environment. [ABSTRACT FROM AUTHOR]

Macroinvertebrates play a vital role in coastal ecosystems and are an important indicator of ecosystem quality. Both anthropogenic activity and environmental changes may lead to significant changes in the marine macroinvertebrate community. However, the assembly process of benthic biodiversity and its mechanism driven by environmental factors at large scales remains unclear. Here, using the benthic field survey data of 15 years at large spatial and temporal scales from the Yellow Sea Large Marine Ecosystem, we investigated the relative importance of environmental selection, dispersal processes, random‐deterministic processes of macroinvertebrates community diversity assembly, and the responses of this relative importance driven by temperature and nutrients. Results showed that the macroinvertebrates community diversity is mainly affected by dispersal. Nitrogen and phosphorus are the most important negative factors among environmental variables, while geographical distance is the main limiting factor of β diversity. Within the range of 0.35–0.70 mg/L of nutrients, increasing nutrient concentration can significantly facilitate the contribution of the decay effect to β diversity. Within the temperature range studied (15.0–18.0°C), both warming and cooling can lead to a greater tendency for species diversity assembly processes to be dominated by deterministic processes. The analysis contributes to a better understanding of the assembly process of the diversity of coastal marine macroinvertebrates communities and how they adapt to global biogeochemical processes. [ABSTRACT FROM AUTHOR]

Leymus chinensis is a dominant grass widely distributed in Central Asia, in both saline−alkaline and non‐saline−alkaline grasslands. However, the mechanisms underlying its saline−alkaline tolerance have not been explored from the perspective of rhizosphere microbial communities. We investigated L. chinensis rhizosphere microbial communities in both saline–alkaline and non‐saline–alkaline grasslands. It was found that the biomass of L. chinensis was remarkably higher in saline–alkaline than in non‐saline–alkaline habitat and that changes in the rhizosphere bacterial and arbuscular mycorrhizal fungi (AMF) communities had a greater effect on biomass than climate, soil moisture, nutrients, and salinity. We demonstrated that the bacteria and AMF in the rhizosphere of L. chinensis grown in saline–alkaline grassland differed from those in non‐saline–alkaline grassland, and the differences were associated with soil salinity or alkalinity. The co‐occurrence networks of bacteria and AMF and bacteria–AMF interaction networks in rhizosphere were complex and connected, with more nodes and edges and a higher average degree of nodes and modularity in the saline–alkaline grassland. More complex networks promoted plant tolerance and growth under salt–alkali stress. High number of microbial keystone taxa was related to the nutrient concentration in the soil and L. chinensis leaves, and more remarkable direct effects of the bacterial and AMF keystone communities on plant nutrient concentrations were demonstrated in saline–alkaline grassland. This indicates that bacterial and AMF communities in saline–alkaline grasslands are favorable for plant growth and nutrient uptake. This study provides an accurate and beneficial source of soil microbial assemblages for future plant–microbial joint remediation of the saline–alkaline ecosystems. [ABSTRACT FROM AUTHOR]

Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22–56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms’ relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.

Abstract Macroinvertebrates play a vital role in coastal ecosystems and are an important indicator of ecosystem quality. Both anthropogenic activity and environmental changes may lead to significant changes in the marine macroinvertebrate community. However, the assembly process of benthic biodiversity and its mechanism driven by environmental factors at large scales remains unclear. Here, using the benthic field survey data of 15 years at large spatial and temporal scales from the Yellow Sea Large Marine Ecosystem, we investigated the relative importance of environmental selection, dispersal processes, random‐deterministic processes of macroinvertebrates community diversity assembly, and the responses of this relative importance driven by temperature and nutrients. Results showed that the macroinvertebrates community diversity is mainly affected by dispersal. Nitrogen and phosphorus are the most important negative factors among environmental variables, while geographical distance is the main limiting factor of β diversity. Within the range of 0.35–0.70 mg/L of nutrients, increasing nutrient concentration can significantly facilitate the contribution of the decay effect to β diversity. Within the temperature range studied (15.0–18.0°C), both warming and cooling can lead to a greater tendency for species diversity assembly processes to be dominated by deterministic processes. The analysis contributes to a better understanding of the assembly process of the diversity of coastal marine macroinvertebrates communities and how they adapt to global biogeochemical processes.

Prokaryotic communities play important roles in sewer sediment ecosystems, but the community composition, functional potential, and assembly mechanisms of sewer sediment prokaryotic communities are still poorly understood. Here, we studied the sediment prokaryotic communities in different urban functional areas (multifunctional, commercial, and residential areas) through 16S rRNA gene amplicon sequencing. Our results suggested that the compositions of prokaryotic communities varied significantly among functional areas. Desulfomicrobium, Desulfovibrio, and Desulfobacter involved in the sulfur cycle and some hydrolytic fermentation bacteria were enriched in multifunctional area, while Methanospirillum and Methanoregulaceae, which were related to methane metabolism were significantly discriminant taxa in the commercial area. Physicochemical properties were closely related to overall community changes (p < 0.001), especially the nutrient levels of sediments (i.e., total nitrogen and total phosphorus) and sediment pH. Network analysis revealed that the prokaryotic community network of the residential area sediment was more complex than the other functional areas, suggesting higher stability of the prokaryotic community in the residential area. Stochastic processes dominated the construction of the prokaryotic community. These results expand our understanding of the characteristics of prokaryotic communities in sewer sediment, providing a new perspective for studying sewer sediment prokaryotic community structure.

Fungal communities play a key role in the decomposition of crop residues and affect soil organic carbon (SOC) dynamics. Conservation tillage enhances SOC sequestration and mitigate global climate change. However, the impact of long-term tillage practices on fungal community diversity and its relation to SOC stock remains unclear. The objectives of this study were to evaluate the relationship between extracellular enzyme activities and fungal community diversity and SOC stock under different tillage practices. A field experiment was conducted with four tillage practices: (i) no-tillage with straw removal (NT0), (ii) no-tillage with straw retention (NTSR, conservation tillage), (iii) plough tillage with straw retention (PTSR), and (iv) rotary tillage with straw retention (RTSR). The results showed that the SOC stock in NTSR was higher than other treatments in the 0–10 cm soil layer. Compared to NT0, NTSR significantly increased soil β-glucosidase, xylosidase, cellobiohydrolase, and chitinase activities at 0–10 cm soil depth (P < 0.05). However, different tillage methods with straw returning had no significant effects on enzyme activity at 0–10 cm soil depth. The observed species and Chao1 index of the fungal communities under NTSR were 22.8% and 32.1% lower than under RTSR in the 0–10 cm soil layer, respectively. The composition, structure, and co-occurrence network of fungal communities differed across tillage practices. A partial least squares path model (PLS-PM) analysis indicated that C-related enzymes were the most influential factors associated with SOC stock. Soil physicochemical properties and fungal communities affected extracellular enzyme activities. Overall, conservation tillage can promote surface SOC stock, which was associated with increased enzyme activity. [ABSTRACT FROM AUTHOR]

Computerized tomography (CT) scan images are widely used in automatic lung cancer detection and classification. The lung nodules’ texture distribution throughout the CT scan volume can vary significantly, and accurate identification and consideration of discriminative information in this volume can greatly help the classification process. Deep stacks of recurrent and convolutional operations cannot entirely represent such variations, especially in the size and location of the nodules. To model this complex pattern of inter/intra dependencies in the CT slices of each nodule, a multi-orientation-based guided-attention module (MOGAM) is proposed in this paper, which provides high flexibility in concentrating on the relevant information extracted from different regions of the nodule in a non-local manner. Moreover, to provide the model with finer-grained discriminative information from the nodule volume, specifically-designed local texture feature descriptors (TFDs) are extracted from the nodule slices in multiple orientations. These TFDs not only represent the distribution of textural information across multiple slices of a nodule but also encode and approximate this distribution within each slice. The extended experimentation has shown the effectiveness of the non-local combination of these local TFDs through the proposed guided attention mechanism. According to the classification results obtained on the standard LIDC-IDRI dataset, the proposed approach has outperformed other counterparts in terms of accuracy and AUC evaluation metrics. Also, a detailed explainability analysis of the results is provided, demonstrating the correct functioning of the proposed attention-based fusion approach, which is required by medical experts.

Abstract Background Diarrhea is a major cause of morbidity and mortality in young calves, resulting in considerable economic loss for dairy farms. To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning, we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials, with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1. Results Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices. Two diarrhea peaks were observed during the transition of the three age periods. Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning, and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage. In the neonatal calves, Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), and Alloprevotella (ASV14) were negatively associated with Clostridium_sensu_stricto_1 (ASV48), the keystone taxa of the diarrhea-phase module. During weaning, unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Barnesiella (ASV497), and Ruminococcaceae_UCG-005 (ASV254) were identified being associated with non-diarrheic status, and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae (ASV28) and Barnesiella (ASV497) had a direct negative relationship with the members of the diarrhea module. Conclusions Taken together, our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea, and some species of Prevotella might be the core microbiota in both neonatal and weaning calves, while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea. Some ASVs affiliated with Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), Alloprevotella (AVS14), unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Ruminococcaceae_UCG-005 (ASV254), and Barnesiella (ASV497) might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1 (ASV48) might be the biomarker for diarrhea risk in specific commercial farms.

Different types of subsidence lakes formed by underground coal mining are severely polluted by mine-production wastewater, domestic sewage, and agricultural irrigation water. Microbial communities perform a crucial role in biogeochemical cycling processes and responses to natural and anthropogenic disturbances in lake waters. Therefore, it is important to investigate the characteristics of microbial community diversity in subsidence lakes for the utilization of water resources in mining areas. In this study, we collected water samples from open and closed subsidence lakes and explored the bacterial communities based on Illumina amplicon high-throughput sequencing. Results showed that bacterial diversity and community and functional composition in open and closed lakes differed greatly, and the bacterial diversity in open lakes was significantly higher than that in closed lakes (p < 0.001). Canonical correspondence analysis found that pH explained 31.73% and 39.98% of the variation in the bacterial community and functional composition in closed lakes, while NH4+ and COD accounted for 29.73% and 26.02% of the changes in the community and functional composition in open lakes, respectively. Modified stochasticity ratios based on null-model analysis demonstrated that stochastic processes were the main factor affecting bacterial community assembly in both closed (MST = 0.58) and open lakes (MST = 0.63). In the closed-lake network, hgcI_clade was inferred to be a keystone species, while Lactococcus, Acinetobacter, Psychrobacter, and Chryseobacterium were detected as keystone species in the open-lake network. By way of discussion, we provide evidence regarding the bacterial community diversity, structure, co-occurrence patterns, and assembly processes in closed and open subsidence lakes. This study contributes to providing a reference for the utilization of subsidence water resources. [ABSTRACT FROM AUTHOR]

Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system. [ABSTRACT FROM AUTHOR]

Automatic image annotation is a method of assigning caption to images that provide some convenient way to index, retrieve and handle a large amount of data objects. It focuses on recent agricultural automation applications; it finds potential in classification along with contextual labeling of the involved objects or detailing based on its statistical properties on fruit categories. However, producing hierarchical labels provide details of a particular fruit subcategory. This paper proposes fruit annotation in a broad sense along with its hierarchical features that can be narrowed down to inherit, further achieving fruit classification into binary or multiple classes indicating subcategories of that fruit. The fruit objects within images are measured to its actual size in the required units. The classification is also used for identifying true color, texture, size, deep features and shape based on the ratio of major to minor axis helpful for fruit gradations. The co-occurrence patterns are obtained based on the visual features of the selected fruit. This is useful for finding the fruit quality categories and combined properties that are used to form the co-occurrence patterns. These patterns are further used by the classifier for fruit annotation. The evaluation of the performance is carried out using the F1 score, accuracy, precision, recall and G-measure. The results show that the co-occurrence pattern with SVM provides an overall accuracy of 97.3% and 97.2% for grape and mango fruit subcategories. The comparative results are obtained to cross-check with the subjective evaluation of gradation validated by local farmers.

ABSTRACT Biochar soil amendments are attracting attention as one strategy to improve soil microbially ecological environment and regulate the soil nitrogen cycle. This study aimed to evaluate the effects of biochar application on agricultural soil improvement, nitrogen (N) mineralization and nitrification. The experiment was carried out on a typical farmland containing black soil and saline-alkaline soil in Northeast China. Four treatments were undertaken, including the control-treated black soil farmland (CS), the biochar-treated black soil farmland (BCS), the control-treated saline-alkali soil farmland (SAS), and the biochar-treated saline-alkaline soil farmland (BSAS). Basic physical and chemical properties, enzyme activity, and the contents of ammonium-nitrogen (NH4+-N) and nitrate-nitrogen (NO3--N) in the soil were subsequently determined. The co-occurrence networks of bacterial communities of the biochar and control treatment groups were constructed based on high-throughput sequencing data of the 16S rRNA genes. The results showed that the BCS and BSAS treatments significantly increased the contents of soil organic matter, total nitrogen, total phosphorus, and available phosphorus. The application of biochar significantly increased the NH4+-N contents in the black soil and saline-alkaline soil by 81.78 and 80.08 %, respectively, while significantly reducing the soil NH4+-N/NO3--N content, which promoted the transformation of NH4+-N into NO3--N. Subsequently, the released NH4+-N was transformed into NO3--N through nitrification. After the biochar application, the NO3--N contents in the black and saline-alkaline soils could be fixed. The biochar application significantly increased the abundance of gdh, AOA-amoA, AOB-amoA, nirK, nirS, nosZ, and nifH genes, with no significant difference in the abundance of napA genes being found among different treatments. Microbes playing a key role in the co-occurrence network were Proteobateria, Acidobacteria, Bacteroidetes, Actinobacteria, and Chloroflexi. As compared with the CS and SAS treatments, under the BCS+BSAS treatment, the connectors, module hubs, connectedness, and clustering coefficient showed larger parameters, and the networks were more complex. The application of biochar gradually increased the nodes, edges, and average degree of the bacterial co-occurrence network, thus indicating that the interaction between microbial groups in the black and saline-alkaline soils post biochar application may be important in the biogeochemical cycle process in farmland soil.

Particle-attached (PA) and free-living (FL) bacterial communities are sensitive to pollutant concentrations and play an essential role in biogeochemical processes and water quality maintenance in aquatic ecosystems. However, the spatiotemporal variations, assembly processes, co-occurrence patterns, and environmental interactions of PA and FL bacteria in drinking water reservoirs remain as yet unexplored. To bridge this gap, we collected samples from 10 sites across four seasons in Lake Tianmu, a large drinking water reservoir in China. Analysis of 16S rRNA gene libraries demonstrated spatiotemporal variations in bacterial diversity and identified differences in bacterial community composition (BCC) between PA and FL lifestyles. Capacity for nitrogen respiration, nitrogen fixation, and nitrate denitrification was enriched in the PA lifestyle, while photosynthesis, methylotrophy, and methanol oxidation were enriched in the FL lifestyle. Deterministic processes, including interspecies interactions and environmental filtration, dominated the assembly of both PA and FL bacterial communities. The influence of environmental filtration on the FL community was stronger than that on the PA community, indicating that bacteria in the FL lifestyle were more sensitive to environmental variation. Co-occurrence patterns and keystone taxa differed between PA and FL lifestyles. The ecological functions of keystone taxa in the PA lifestyle were associated with the supply and recycling of nutrients, while those in FL were associated with the degradation of complex pollutants. PA communities were more stable than FL communities in the face of changing environmental conditions. Nutrients (e.g., TDN and NO3-) and abiotic and biotic factors (e.g., WT and Chl-a) exerted positive and negative effects, respectively, on the co-occurrence networks of both lifestyles. These results improve our understanding of assembly processes, co-occurrence patterns, and environmental interactions within PA and FL communities in a drinking water reservoir. [ABSTRACT FROM AUTHOR]

Background: Diarrhea is a major cause of morbidity and mortality in young calves, resulting in considerable economic loss for dairy farms. To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning, we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials, with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1. Results: Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices. Two diarrhea peaks were observed during the transition of the three age periods. Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning, and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage. In the neonatal calves, Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), and Alloprevotella (ASV14) were negatively associated with Clostridium_sensu_stricto_1 (ASV48), the keystone taxa of the diarrhea-phase module. During weaning, unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Barnesiella (ASV497), and Ruminococcaceae_UCG-005 (ASV254) were identified being associated with non-diarrheic status, and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae (ASV28) and Barnesiella (ASV497) had a direct negative relationship with the members of the diarrhea module. Conclusions: Taken together, our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea, and some species of Prevotella might be the core microbiota in both neonatal and weaning calves, while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea. Some ASVs affiliated with Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), Alloprevotella (AVS14), unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Ruminococcaceae_UCG-005 (ASV254), and Barnesiella (ASV497) might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1 (ASV48) might be the biomarker for diarrhea risk in specific commercial farms. [ABSTRACT FROM AUTHOR]

Release of nanoceria (nCeO2) into the environment has caused much concern about its potential toxicity, which still remains poorly understood for soil microorganisms. In this study, nanoceria and cerium (III) nitrate at different doses (10, 100 and 500 mg/kg) were applied to bok choy (Brassica rapa subsp. chinensis), grown in potting soil, to investigate the responses of soil bacterial communities to nanoceria (NC) and ionic cerium (IC) applications. The results showed that bacterial richness was slightly increased in all cerium treatments relative to the negative control without cerium amendment (CK), but a significant increase was only found in IC500. The patterns of bacterial community composition, predicted functions and phenotypes of all NC treatments were significantly differentiated from IC and CK treatments, which was correlated with the contents of cerium, available potassium and phosphorus in soil. The co-occurrence network of bacterial taxa was more complex after exposure to ionic cerium than to nanoceria. The keystone taxa of the two networks were entirely different. Predicted functions analysis found that anaerobic and Gram-negative bacteria were enriched under nanoceria exposure. Our study implies that Proteobacteria and nitrifying bacteria were significantly enriched after exposure to nanoceria and could be potential biomarkers of soil environmental perturbation from nanoceria exposure. [ABSTRACT FROM AUTHOR]

Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less intertaxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations. [ABSTRACT FROM AUTHOR]

Coastal reclamation is a global threat to coastal wetland ecosystems, but the impacts of coastal reclamation on belowground biodiversity and their consequences for ecosystem nutrient cycling remain poorly understood. In this study, we examined soil bacterial communities, bacterial co-occurrence pattern and soil multi-nutrient cycling index after natural vegetated coastal wetlands were converted for 6-year and 30-year rice-wheat rotation fields. The soil multi-nutrient cycling index was higher in 6-year and 30-year rice-wheat rotation fields than natural vegetated coastal wetlands. For bacterial community, rice-wheat rotation reclamation increased soil bacterial alpha diversity but decreased beta diversity and co-occurrence network complexity than those in the vegetated coastal wetland. Rice-wheat rotation reclamation also changed soil bacterial community assemblages by increasing the relative abundance of Actinobacteriota and Desulfobacterota while decreasing the relative abundance of Alphaproteobacteria and Gammproteobacteria. Changes in the relative importance of dispersal limitation and homogenizing dispersal mainly controlled the variations in soil bacterial community assemblages. Soil bacterial community variations induced by rice-wheat reclamation were strongly related to soil multi-nutrient cycling, especially bacterial connection complexity. Our results provide experimental support that belowground microbial interactions are crucial for maintaining ecosystem functioning.

This paper provides an estimation of the hazard related to the presence of furan and five alkyl furans (2- and 3-methylfuran, 2-ethylfuran, 2,5- and 2,3-dimethylfuran) in foodstuffs available in the Belgian market. To achieve this objective, a specific sampling plan was designed to ensure that the samples collected (n = 1003) represent the diversity of the Belgian food chain. Herein, the concepts of the Hazard Ratio of a sample (HRs) and the Hazard Index of a sample (HIs) were introduced to primarily characterize the hazard related to the co-occurrence of these compounds. The HRs was measured as the ratio of the potential daily exposure to a substance (expressed in mg/Kg of food) to both the 10% reference dose level for chronic effects (expressed in mg/(kg b.w*day)) and the human standard weight (expressed in kg). Whereas the HIs is the sum of the HRs of compounds that affect the same target organ/system, a hazard index greater than one indicates a highly contaminated matrix that could induce a hazard. It is an alarm indicating that additional attention should be given to this matrix. This may involve additional analyses to confirm the high level, to identify sources, etc. It is also an alarm for the risk assessor to be very careful with flagged matrices and to avoid combination with other matrices. The HIs highlight a relatively low concern for all foods analyzed (HI median < 1.0) with a relatively higher suspected hazard for coffee drinks (HI median = 0.068, HI max = 0.57). This preliminary estimation of the potential hazard suggests that coffee beverages should be examined in more detail in a full risk assessment and that coffee consumption should be taken with caution given the levels of furan and alkylfurans reported in this study. [ABSTRACT FROM AUTHOR]

Body size determines individuals' life history and metabolic rates and thus, regulates community-level dynamics. However, whether body size mediates community co-occurrences and stability, especially in complex communities across different microbial trophic levels, remains unknown. Here, we investigate whether body size determines the co-occurrence pattern and stability of microbial communities across local, regional, and continental scales in the paddy soil ecosystems. Soil samples were collected from rice paddy fields at multiple spatial scales, and soil microbial communities were subsequently sequenced. The microorganisms were then divided into different groups based on taxonomic information at phylum/subphylum level, and the average body size of each microbial group was identified based on propagule size from documented literature. We examined the relationships between microbial body size and various community traits such as potential migration rate, co-occurrence pattern, cohesion, and community stability. Our results consistently showed that the small-sized microorganisms such as bacteria had significantly higher niche breadth, niche overlap and migration rate at various spatial scales. We found that microbial body size is consistently negatively correlated to negative co-occurrences and community stability. Our results, for the first time, put microbial body size into a broader community ecology framework, and contribute to a greater understanding of how microbial taxa with different body sizes would respond to future changes and perturbations. [ABSTRACT FROM AUTHOR]

Automatic image annotation is a method of assigning caption to images that provide some convenient way to index, retrieve and handle a large amount of data objects. It focuses on recent agricultural automation applications; it finds potential in classification along with contextual labeling of the involved objects or detailing based on its statistical properties on fruit categories. However, producing hierarchical labels provide details of a particular fruit subcategory. This paper proposes fruit annotation in a broad sense along with its hierarchical features that can be narrowed down to inherit, further achieving fruit classification into binary or multiple classes indicating subcategories of that fruit. The fruit objects within images are measured to its actual size in the required units. The classification is also used for identifying true color, texture, size, deep features and shape based on the ratio of major to minor axis helpful for fruit gradations. The co-occurrence patterns are obtained based on the visual features of the selected fruit. This is useful for finding the fruit quality categories and combined properties that are used to form the co-occurrence patterns. These patterns are further used by the classifier for fruit annotation. The evaluation of the performance is carried out using the F1 score, accuracy, precision, recall and G-measure. The results show that the co-occurrence pattern with SVM provides an overall accuracy of 97.3% and 97.2% for grape and mango fruit subcategories. The comparative results are obtained to cross-check with the subjective evaluation of gradation validated by local farmers. [ABSTRACT FROM AUTHOR]

Bacterial biodiversity is tightly correlated with ecological functions of natural systems, and bacterial rare and abundant subcommunities make distinct contributions to ecosystem functioning. However, the biogeographic pattern and elevational differentiation of sedimentary bacterial diversity have rarely been studied in cross-river systems at a continental scale. This study analyzed the biogeographic patterns and elevational differentiations of the entire, abundant, and rare bacterial (sub) communities as well as the underlying mechanisms across nine rivers that span distinct geographic regions and large elevational gradients in China. We found that bacterial rare and abundant subcommunities shared similar biogeographic patterns and both demonstrated strong distance-decay relationships, despite their distinct community compositions. However, both null model and variation partitioning analysis results showed that while environmental selection governed rare subcommunity assemblies (contribution: 51.9%), dispersal limitation (62.7%) controlled the assembly of abundant subcommunities. The disparity was associated with the broader threshold width of abundant taxa to water temperature and pH variations than rare taxa. Elevation-induced bacterial composition variations were more evident than latitudeinduced ones. Some specific operational taxonomic units (OTUs), representing 16.4% of the total sequences, much preferentially and even exclusively lived in high-elevation or low-elevation habitats and demonstrated some adaptations to local conditions. Greater positive: negative link ratios in bacterial co-occurrence networks of low elevations than high elevations (P < 0.05) partly resulted from their harboring higher organic carbon: nitrogen ratios. Together, this study draws a biogeographic picture of sedimentary bacterial communities in a continental-scale riverine system and highlights the importance of incorporating elevation-associated patterns of microbial diversity into riverine microbial ecology studies. [ABSTRACT FROM AUTHOR]

Macroalgae interact with planktonic microbes in seawater. It remains unclear how planktonic microbes interact with the environment and each other during the cultivation processes of commercially important algal species. Such an interaction is important for developing environment-friendly mariculture methods. In this study, the dynamics of the planktonic microbial community associated with Saccharina japonica were profiled during the seedling production stage, with its environmental correlation and co-occurrence pattern determined simultaneously. Microbial richness increased and positively correlated with light intensity and contents of NO3− and PO43−. A clear temporal succession of the community was observed, which coincided with changes in light intensity, dissolved oxygen, pH, and NO3− content. α-Proteobacteria, Bacteroidetes, γ-Proteobacteria, and the genera prevalent in these taxa dominated the planktonic microbial community, and their relative abundance temporally changed. A profile of keystone taxa that is different from prevalent genera was identified based on betweenness centrality scores. A modularized co-occurrence pattern was determined, in addition to intensified species-to-species interactions at the core of the co-occurrence network. These findings expanded our cognization of the planktonic microbial community in response to S. japonica cultivation. [ABSTRACT FROM AUTHOR]

Different types of subsidence lakes formed by underground coal mining are severely polluted by mine-production wastewater, domestic sewage, and agricultural irrigation water. Microbial communities perform a crucial role in biogeochemical cycling processes and responses to natural and anthropogenic disturbances in lake waters. Therefore, it is important to investigate the characteristics of microbial community diversity in subsidence lakes for the utilization of water resources in mining areas. In this study, we collected water samples from open and closed subsidence lakes and explored the bacterial communities based on Illumina amplicon high-throughput sequencing. Results showed that bacterial diversity and community and functional composition in open and closed lakes differed greatly, and the bacterial diversity in open lakes was significantly higher than that in closed lakes (p < 0.001). Canonical correspondence analysis found that pH explained 31.73% and 39.98% of the variation in the bacterial community and functional composition in closed lakes, while NH4+ and COD accounted for 29.73% and 26.02% of the changes in the community and functional composition in open lakes, respectively. Modified stochasticity ratios based on null-model analysis demonstrated that stochastic processes were the main factor affecting bacterial community assembly in both closed (MST = 0.58) and open lakes (MST = 0.63). In the closed-lake network, hgcI_clade was inferred to be a keystone species, while Lactococcus, Acinetobacter, Psychrobacter, and Chryseobacterium were detected as keystone species in the open-lake network. By way of discussion, we provide evidence regarding the bacterial community diversity, structure, co-occurrence patterns, and assembly processes in closed and open subsidence lakes. This study contributes to providing a reference for the utilization of subsidence water resources.

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus , Prevotellaceae , and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome. [Display omitted] • Soluble nutrients had a greater effect on altering gut microbiota than insoluble forms. • Differing in high diversity of ARGs in old pandas, the young had more ARG abundance. • Shared 85 ARGs and 21 MGEs were identified in soil, bamboo, and giant panda guts. • Bacterial community and MGEs were stronger than diet in shaping ARG profile. [ABSTRACT FROM AUTHOR]

Indigenous soil microbial biomass (ISMB) plays a key role in maintaining essential functions and biodiversity of soil health. One of the critical unknowns is how the indigenous microorganisms respond to different fertilizers which is directly related to agricultural production. Therefore, we used Mi-Seq sequencing and network analyses to compare the response of ISMB to biogas residue and chemical fertilizers. The results showed that crop production was profoundly influenced by levels of ISMB present and is further dependent on the strategy of fertilizer application. Higher ISMB primarily manifests through retention of richer microbial abundance, a balanced community structure, and tightened co-occurrence within a certain proportion of Nitrospirae, Rhizophlyctidaceae, and Gemmatimonadetes. Compared to chemical fertilizer, biogas residue resulted in higher production with more strongly linked nodes such as Actinobacteria, Chloroflexi and Gemmatimonadetes. Under the same level of ISMB, the microbial diversity was richer and co-occurrence was tighter when biogas residues were applied compared with chemical fertilizer. In addition, the higher level of ISMB with biogas residue applied had a lower abundance of potential fungal pathogens in both bulk and rhizosphere soil compared with chemical fertilizer. This study provides critical data to understand the influence of ISMB and biogas residue on soil ecological system.

Microbes play an essential role in agricultural ecosystems; however, the processes that drive the microbial biogeographic and co-occurrence patterns have rarely been assessed simultaneously, especially in the broomcorn millet rhizosphere. In this work, we explored the spatial distribution and association networks of bacteria and fungi in the rhizosphere of broomcorn millet selected from 12 locations across northern China using high-throughput sequencing. We decomposed the β-diversity into species turnover and nestedness, confirming that the bacterial and fungal β-diversity in the broomcorn millet rhizosphere was almost entirely linked to species turnover. Distance-decay relationships revealed that the biogeographic patterns of rhizosphere bacterial and fungal β-diversity (including species turnover rather than nestedness) were clearly distinct. Environmental selection was the only factor determining the rhizosphere bacterial β-diversity, whereas the rhizosphere fungal β-diversity was governed by both environmental selection and dispersal limitation. We also demonstrated that mean annual temperature (MAT) and pH were the major ecological drivers regulating the bacterial and fungal community structure, keystone species, and modularisation in the broomcorn millet rhizosphere. This elucidated different mechanisms of bacterial and fungal biogeographic and co-occurrence patterns in the broomcorn millet rhizosphere, and provided new ideas and basic insights for an in-depth understanding of the biogeography and coexistence theory of broomcorn millet rhizosphere ecosystems. [ABSTRACT FROM AUTHOR]

Conservation tillage is an advanced agricultural technology that seeks to minimize soil disturbance by reducing, or even eliminating tillage. Straw or stubble mulching in conservation tillage systems help to increase crop yield, maintain biodiversity and increase levels of exogenous nutrients, all of which may influence the structure of fungal communities in the soil. Currently, however, the assembly processes and co-occurrence patterns of fungal sub-communities remain unknown. In this paper, we investigated the effects of no-tillage and straw mulching on the composition, assembly process, and co-occurrence patterns of soil fungal sub-communities in a long-term experimental plot (15 years). The results revealed that combine straw mulching with no-tillage significantly increased the richness of fungi but not their diversity. Differential abundance analysis and principal component analysis (PCA) indicated that tillage management had a greater effect on the fungal communities of abundant and intermediate taxa than on the rare taxa. Available phosphorus (AP) and total nitrogen (TN) were the major determinants of fungal sub-communities in NT treatment. The abundant fungal sub-communities were assembled by deterministic processes under medium strength selection, while strong conservation tillage strength shifts the abundant sub-community assembly process from deterministic to stochastic. Overall, the investigation of the ecological network indicated that no-tillage and straw mulching practices decreased the complexity of the abundant and intermediate fungal networks, while not significantly influencing rare fungal networks. These findings refine our knowledge of the response of fungal sub-communities to conservation tillage management techniques and provide new insights into understanding fungal sub-community assembly. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities are vital for plant growth and soil sustainability; however, the composition of rhizobacterial communities, especially the assembly process and co-occurrence pattern among microbiota after the inoculation of some beneficial bacteria, remains considerably unclear. In this study, we investigated the structure of rhizomicrobial communities, their assembly process, and interactions contrasting when Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 are co-inoculated or Bradyrhizobium japonicum 5038 mono-inoculated in black and cinnamon soils of soybean fields. The obtained results indicated that the Chao and Shannon indices were all higher in cinnamon soil than that in black soil. In black soil, the co-inoculation increased the Shannon indices of bacteria comparing with that of the mono-inoculation. In cinnamon soil, the co-inoculation decreased the Chao indices of fungi comparing with that of mono-inoculation. Compared with the mono-inoculation, the interactions of microorganisms of co-inoculation in the co-occurrence pattern increased in complexity, and the nodes and edges of co-inoculation increased by 10.94, 40.18 and 4.82, 16.91% for bacteria and fungi, respectively. The co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 increased the contribution of stochastic processes comparing with Bradyrhizobium japonicum 5038 inoculation in the assembly process of soil microorganisms, and owing to the limitation of species diffusion might restrict the direction of pathogenic microorganism movement. These findings support the feasibility of rebuilding the rhizosphere microbial system via specific microbial strain inoculation and provide evidence that the co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 can be adopted as an excellent compound rhizobia agent resource for the sustainable development of agriculture. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial communities are vital for plant growth and soil sustainability; however, the composition of rhizobacterial communities, especially the assembly process and co-occurrence pattern among microbiota after the inoculation of some beneficial bacteria, remains considerably unclear. In this study, we investigated the structure of rhizomicrobial communities, their assembly process, and interactions contrasting when Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 are co-inoculated or Bradyrhizobium japonicum 5038 mono-inoculated in black and cinnamon soils of soybean fields. The obtained results indicated that the Chao and Shannon indices were all higher in cinnamon soil than that in black soil. In black soil, the co-inoculation increased the Shannon indices of bacteria comparing with that of the mono-inoculation. In cinnamon soil, the co-inoculation decreased the Chao indices of fungi comparing with that of mono-inoculation. Compared with the mono-inoculation, the interactions of microorganisms of co-inoculation in the co-occurrence pattern increased in complexity, and the nodes and edges of co-inoculation increased by 10.94, 40.18 and 4.82, 16.91% for bacteria and fungi, respectively. The co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 increased the contribution of stochastic processes comparing with Bradyrhizobium japonicum 5038 inoculation in the assembly process of soil microorganisms, and owing to the limitation of species diffusion might restrict the direction of pathogenic microorganism movement. These findings support the feasibility of rebuilding the rhizosphere microbial system via specific microbial strain inoculation and provide evidence that the co-inoculation of Bradyrhizobium japonicum 5038 and Bacillus aryabhattai MB35-5 can be adopted as an excellent compound rhizobia agent resource for the sustainable development of agriculture.

Conservation tillage is an advanced agricultural technology that seeks to minimize soil disturbance by reducing, or even eliminating tillage. Straw or stubble mulching in conservation tillage systems help to increase crop yield, maintain biodiversity and increase levels of exogenous nutrients, all of which may influence the structure of fungal communities in the soil. Currently, however, the assembly processes and co-occurrence patterns of fungal sub-communities remain unknown. In this paper, we investigated the effects of no-tillage and straw mulching on the composition, assembly process, and co-occurrence patterns of soil fungal sub-communities in a long-term experimental plot (15 years). The results revealed that combine straw mulching with no-tillage significantly increased the richness of fungi but not their diversity. Differential abundance analysis and principal component analysis (PCA) indicated that tillage management had a greater effect on the fungal communities of abundant and intermediate taxa than on the rare taxa. Available phosphorus (AP) and total nitrogen (TN) were the major determinants of fungal sub-communities in NT treatment. The abundant fungal sub-communities were assembled by deterministic processes under medium strength selection, while strong conservation tillage strength shifts the abundant sub-community assembly process from deterministic to stochastic. Overall, the investigation of the ecological network indicated that no-tillage and straw mulching practices decreased the complexity of the abundant and intermediate fungal networks, while not significantly influencing rare fungal networks. These findings refine our knowledge of the response of fungal sub-communities to conservation tillage management techniques and provide new insights into understanding fungal sub-community assembly.

ABSTRACT The Loess Plateau is located in the arid and semi-arid regions in northern China. The ecosystem is particularly sensitive to natural and anthropogenic disturbances. Fungi can produce extracellular enzymes, decompose a variety of organic matter, and regulate carbon and nutrient balance. We studied the changes of soil fungal community compositions in response to straw, inorganic fertilizer, and compost in a typical farmland in the Loess Plateau. Our results demonstrated that the addition of straw significantly reduces the Shannon index of the fungal community, in addition, the participation of straw significantly affects the composition of the fungal community. Functional prediction based on FUNGuild showed that straw significantly reduced the relative abundance of saprotrophs, pathotrophs, symbiotrophs, lichenized, ectomycorrhizal, and plant pathogens. Although fertilization practices destroyed the co-occurrence pattern among the fungal species, the addition of straw alleviated this affect. No significant effect of straw, compost, and inorganic fertilizers on the co-occurrence pattern among species in the soil fungal community was observed. Compared with compost and inorganic fertilizer, the addition of straw shaped the community composition by changing the relative abundance of fungal functional taxa. Thus, in the fragile Loess Plateau environment, over-fertilizing or non-order-fertilizing may destroy the co-occurrence pattern of the fungal communities and Loess Plateau ecosystem. IMPORTANCE Determining the response of soil fungi in sensitive ecosystems to external environmental disturbances is an important, yet little-known, topic in microbial ecology. In this study, we evaluated the impact of traditional fertilization management practices on the composition, co-occurrence pattern, and functional groups of fungal communities in loessial soil. Our results show that in the fragile Loess Plateau environment, fertilizer management changed the composition of the fungal community and disrupted the co-occurrence pattern between fungi. The application of straw alleviates the destroying of the co-occurrence pattern. The current research emphasizes the necessity of rational fertilization of farmland in loessial soil.

Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

Release of nanoceria (nCeO2) into the environment has caused much concern about its potential toxicity, which still remains poorly understood for soil microorganisms. In this study, nanoceria and cerium (III) nitrate at different doses (10, 100 and 500 mg/kg) were applied to bok choy (Brassica rapa subsp. chinensis), grown in potting soil, to investigate the responses of soil bacterial communities to nanoceria (NC) and ionic cerium (IC) applications. The results showed that bacterial richness was slightly increased in all cerium treatments relative to the negative control without cerium amendment (CK), but a significant increase was only found in IC500. The patterns of bacterial community composition, predicted functions and phenotypes of all NC treatments were significantly differentiated from IC and CK treatments, which was correlated with the contents of cerium, available potassium and phosphorus in soil. The co-occurrence network of bacterial taxa was more complex after exposure to ionic cerium than to nanoceria. The keystone taxa of the two networks were entirely different. Predicted functions analysis found that anaerobic and Gram-negative bacteria were enriched under nanoceria exposure. Our study implies that Proteobacteria and nitrifying bacteria were significantly enriched after exposure to nanoceria and could be potential biomarkers of soil environmental perturbation from nanoceria exposure.

The lakeshore habitat, which is an interface zone between lake and land, harbours various organic particles providing nutrient‐rich microhabitats for bacterial colonisation. Revealing the mechanisms maintaining the bacterial diversity generated on these particles is vital for understanding the biogeochemical processes within lakeshore habitats. To date, however, the bacterial communities within lakeshore habitats have been rarely explored, and knowledge of the ecological processes associated with their spatial distribution is limited.Here, we employed amplicon‐based high throughput sequencing technology to investigate the composition, co‐occurrence patterns, spatial distribution, and assembly processes of free‐living and particle‐attached bacterial communities (FLBC vs. PABC) across 29 lakeshore zones within freshwater lakes from two typical regions: Middle–Lower Yangtze River Plain and Yunnan–Kweichow Plateau.We found significant community dissimilarity between both bacterial lifestyles and regions. PABC exhibited higher community dissimilarity between the plain and plateau regions than FLBC did. Furthermore, eight operational taxonomic units were detected as a core bacterial community within the lakeshore habitats across the plain and plateau regions. Network analysis revealed that bacterial taxa preferring a particle‐attached lifestyle exhibited more co‐occurrence associations for both intra‐ and inter‐community than the free‐living lifestyle. Both FLBC and PABC showed significant distance–decay relationships in these two regions. Dispersal limitation was the most important process associated with patterns in the spatial distribution of FLBC and PABC, whereas the relative importance of variable and homogeneous selection differed between the assembly of FLBC and PABC because of differences in their microhabitats.Our results highlight that dispersal limitation may be strongly associated with the spatial distribution of lakeshore bacterial communities at a regional scale. However, lifestyle differences influence the relative balance between the processes of dispersal, selection, and biotic interaction that influence these bacterial communities.This study reveals potential interactions between bacterial taxa with different lifestyles as well as indicating which ecological processes may lie behind the spatial distribution of bacterial communities in lakeshore habitats. Knowledge of potential assembly mechanisms of bacterial communities within different microhabitats help us understand how bacterial communities in different microhabitats are generated and their different roles in biogeochemical processes in lakeshore habitats. [ABSTRACT FROM AUTHOR]

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us. [ABSTRACT FROM AUTHOR]

This paper provides an estimation of the hazard related to the presence of furan and five alkyl furans (2- and 3-methylfuran, 2-ethylfuran, 2,5- and 2,3-dimethylfuran) in foodstuffs available in the Belgian market. To achieve this objective, a specific sampling plan was designed to ensure that the samples collected (n = 1003) represent the diversity of the Belgian food chain. Herein, the concepts of the Hazard Ratio of a sample (HRs) and the Hazard Index of a sample (HIs) were introduced to primarily characterize the hazard related to the co-occurrence of these compounds. The HRs was measured as the ratio of the potential daily exposure to a substance (expressed in mg/Kg of food) to both the 10% reference dose level for chronic effects (expressed in mg/(kg b.w*day)) and the human standard weight (expressed in kg). Whereas the HIs is the sum of the HRs of compounds that affect the same target organ/system, a hazard index greater than one indicates a highly contaminated matrix that could induce a hazard. It is an alarm indicating that additional attention should be given to this matrix. This may involve additional analyses to confirm the high level, to identify sources, etc. It is also an alarm for the risk assessor to be very careful with flagged matrices and to avoid combination with other matrices. The HIs highlight a relatively low concern for all foods analyzed (HI median < 1.0) with a relatively higher suspected hazard for coffee drinks (HI median = 0.068, HI max = 0.57). This preliminary estimation of the potential hazard suggests that coffee beverages should be examined in more detail in a full risk assessment and that coffee consumption should be taken with caution given the levels of furan and alkylfurans reported in this study.

Aims: In arid regions, the succession of biological soil crusts (biocrusts) usually accompanies substantial turnover of community composition. How interspecific interactions among biocrust-forming mosses, lichens, algae and cyanobacteria change along the successional gradient is largely unknown. According to the stress gradient hypothesis (SGH), the frequency or intensity of facilitative and competitive interactions within the community will vary along an environmental stress gradient, with an increasing role of competition relative to facilitation under more benign environmental conditions. In the process of biocrust succession, decreasing soil stress also occurs because of slow soil amelioration, which meets the assumption of the SGH. Therefore, we hypothesize that the changes in facilitative and competitive interactions within biocrust communities will follow the prediction of the SGH and that the nature of biocrust interactions will also change. Location: Sand-binding vegetation belts for the Baotou–Lanzhou railway at the southeast fringe of the Tengger Desert in the Shapotou region of the Ningxia Hui Autonomous Region, western China. Methods: We conducted a field evaluation at five adjacent sand-binding vegetation belts built in chronosequence to study the successional gradient. Small-scale patterns of co-occurrence and null models were used to evaluate the community-level interspecific interactions among the biocrust-forming mosses, lichens, algae and cyanobacteria. In addition, an accessory method of species-pair co-occurrence based on null models was also applied to potentially identify the nature of the interspecific interactions within the biocrusts and for the causal investigation of these patterns. Results: A strong spatial segregation of co-occurrence patterns occurred between cyanobacteria and algae and species of mosses and lichens at early succession, and occurred among species of mosses and lichens at late succession, while the weak spatial aggregation between lichen species only occurred at middle succession. Conclusions: Negative interspecific interactions were prevalent within biocrusts throughout succession. The co-occurrence patterns at both the community and species-pair levels are consistent, supporting the unimodal version of the SGH that species interactions shift toward competition under extremely stressed conditions. Given the lack of research on interspecific interactions in biocrusts, our study is important for obtaining a deeper understanding of biocrust succession. [ABSTRACT FROM AUTHOR]

Aims: In water-limited areas, shrubs influence biological soil crust (biocrust) composition and diversity via soil microenvironment alterations and through modifying biotic interactions amongst biocrust taxa. However, the relative contributions of shrubs to biocrust succession and assembly via the biotic and abiotic influences are poorly known. Methods: The community composition of biocrusts and soil properties in the interspace and beneath the dominant shrub (Artemisia ordosica) along a biocrust succession sequence were investigated. Biocrust interspecific interactions at a small scale (within shrub) were evaluated based on the co-occurrence pattern using null models. A hypothetical multigroup structural equation model (SEM) was proposed to evaluate the influence of multiple variables on the biocrust richness and to investigate the path variance between successional stages. Results: Along the biocrust succession, shrubs significantly increased the size of bare soil gap by 489%, decreased lichens by 43% and increased soil organic matter by 13%. In years 18, 31and 37, the paths in SEM explained 59% of the variation in richness, only the effect of abiotic amelioration was significant (0.62). In years 54 and 62, the shrubs had direct (0.37) and indirect effect (0.10) via species interaction to biocrust richness. Conclusions: Shrubs directly and indirectly affected the community assembly of biocrusts. Biocrust species interactions are an important driver of biocrust diversity and primarily affect late succession. The increasing influences of shrubs suggests a close relationship between shrub and biocrust components in arid or semiarid ecosystems, with shrubs playing an important role in regulating biocrust assembly and maintaining biocrust richness. [ABSTRACT FROM AUTHOR]

Contamination of alkaline copper mine drainage (AlkCuMD) causes serious damages to riverine ecosystem. Sediment bacterial community, as the fundamental component of biogeochemical processes, has been applied as an effective ecological indicator for various pollutants, but little is known about its relation to AlkCuMD. In this study, the composition variation, indicator species, and co-occurrence pattern of sediment bacterial community were studied in the Jinsha River, a typical AlkCuMD polluted large river in southwestern China. Results showed that significant sulfur (TSmax, 84.06 g/kg) and copper (Cumax, 1.63 g/kg) contamination from AlkCuMD decreased the richness and diversity of bacterial community, and the composition of bacterial community was significantly altered by copper, zinc, chromium, and total organic carbon. Moreover, the indicator species identified in the polluted sediments, including Thiovirga and Symbiobacterium, exhibited the functional traits of sulfur oxidation and metal(loid) cycling; while the indicator species in the unpolluted sediments were mainly associated with the nitrogen and phosphorus biotransformation. In addition, the bacterial co-occurrence pattern showed higher positive interactions and network connectivity at polluted sites, suggesting the potential enhancement of bacterial interspecific mutualistic relationships against AlkCuMD contamination. Therefore, this study provides an important evaluation of AlkCuMD influence on sediment bacterial community, and proposes the potential ecological indicators for evaluating AlkCuMD pollution in river sediments.

Macroalgae interact with planktonic microbes in seawater. It remains unclear how planktonic microbes interact with the environment and each other during the cultivation processes of commercially important algal species. Such an interaction is important for developing environment-friendly mariculture methods. In this study, the dynamics of the planktonic microbial community associated with Saccharina japonica were profiled during the seedling production stage, with its environmental correlation and co-occurrence pattern determined simultaneously. Microbial richness increased and positively correlated with light intensity and contents of NO3− and PO43−. A clear temporal succession of the community was observed, which coincided with changes in light intensity, dissolved oxygen, pH, and NO3− content. α-Proteobacteria, Bacteroidetes, γ-Proteobacteria, and the genera prevalent in these taxa dominated the planktonic microbial community, and their relative abundance temporally changed. A profile of keystone taxa that is different from prevalent genera was identified based on betweenness centrality scores. A modularized co-occurrence pattern was determined, in addition to intensified species-to-species interactions at the core of the co-occurrence network. These findings expanded our cognization of the planktonic microbial community in response to S. japonica cultivation.

Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success—both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada , Ipomoea cairica , Ipomoea pes-caprae , and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities. [ABSTRACT FROM AUTHOR]

The Pollution Nagasaki (PN) section of the East China Sea (ECS) is a typical area for studying the complex hydrographic dynamics between Changjiang River discharge and Kuroshio, displaying intense variations of environmental gradients from nearshore to offshore. However, the temporal and spatial changes of microbial communities along the PN section have long been overlooked. In this study, we performed a comprehensive investigation into the abundance, diversity and ecology of free-living (FL) and particle-associated (PA) microbial communities in seawater samples along the PN section during both summer and winter. Distinct hydrological conditions and resulting environmental gradients were observed between summer and winter, with clear features of intrusive Kuroshio subsurface water in summer and strong vertical mixing of seawater in winter. Bacterial abundance along the PN section was higher in summer (1.11 × 10 8 copies·L -1 - 7.37 × 10 8 copies·L -1 ) than in winter (1.83 × 10 6 copies·L -1 - 1.34 × 10 8 copies·L -1 ). Microbial diversity, as indicated by α-diversity indices, remained at relatively stable levels in summer, while a clear decreasing trend was observed in winter along the PN section. Additionally, the winter communities exhibited a more evident spatial shift along the PN section compared to the summer communities. 16S rRNA gene amplicon sequencing showed that microbial community composition varied considerably between different seasons (summer and winter) and lifestyles (FL and PA), with a notable dominance of Ralstonia species. in winter. Regarding the assembly of microbial communities, the stochastic process represented by dispersal limitation was the dominant process in summer, while the deterministic homogeneous selection was the most important process in winter. Correspondingly, distinct topological properties of the microbial co-occurrence networks were shown between different seasons and along the PN section. These results enhance our understanding of how hydrological conditions influence dynamic changes of microbial communities along the PN section, providing new insights for the microbial community assembly and interactions in such a complex environment., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The handling editor FT declared a past collaboration with the author X-HZ., (Copyright © 2024 Jin, Liu, Zhao, Sun, Tan, Zhang and Zhang.)

Bacteria are important soil components that function as both decomposers and plant symbionts and play a major role in plant–microbe interactions. However, little is known about the diversity of bacterial communities in the rhizosphere of the native invasive plant Echinochloa caudata. In this study, we used high-throughput sequencing to investigate bacterial communities in the rhizospheres of Echinochloa caudata collected from areas with differing degrees of invasion. We found that the rhizosphere microbiome networks had small-world properties and modular structures, and the soil rhizosphere microbial communities differed significantly in the different areas analyzed. We speculate that disturbances (such as grazing) form a sediment-water environment that is beneficial for the colonization of rhizosphere microorganisms and ultimately improves the invasive ability of the species by allowing the occupation of more ecological niches and more diverse functions, eventually promoting Echinochloa caudata invasion in wetland. [ABSTRACT FROM AUTHOR]

Aerobic composting is eco-friendly and sustainable practice for kitchen waste (KW) disposal to restore soil fertility and reduce environmental risks. However, KW compact structure, perishable nature, acidification by anaerobic acidogens, inhibits the metabolism of aerobic microbes, insufficient breakdown of organic matters, and prolong the composting duration. This study, co-composted coal fly ash (FA), to regulate bacterial dynamics, co-occurrence patterns and nutrients transformation in KW composting. Our results indicated, FA created suitable environment by increasing pH and temperature, which facilitated the proliferation and reshaping of microbial community. FA fostered the relative abundances of phlya (Proteobacteria , Chloroflexi and Actinobacteriota) and genera (Bacillus , Paenibacillus and Lysinibacillus), which promoted the nutrients transformation (phosphorus and nitrogen) in KW compost. FA enhanced the mutualistic correlations between bacterial communities, promoted the network complexity (nodes & edges) and contains more positive connections, which reflect the FA amendment effects. KW mature compost seed germination index reached >85% of FA treatment, indicated the final products fully met the Chinese national standard for organic fertilizer. These findings might provide opportunity to advance the KW composting and collaborative management of multiple waste to curb the current environmental challenges. [Display omitted] • Co-composting FA to enhance maturation of KW aerobic composting was investigated. • FA enriched bacterial dynamics and microbial mutualistic interaction in KW compost. • FA minimized the accumulations of toxic heavy metals in KW compost. • Good quality compost with SGI >80% were achieved with FA. [ABSTRACT FROM AUTHOR]

[Display omitted] • The trends in anoxic P-take and dominant taxa abundance were highly similar. • High nitrite stress rapidly promoted the shift of the bacterial community state. • Shift of community state was mostly driven by low modularity and positive links. • OLB8 and Zoogloea functioned crucial roles in resisting nitrite to enhance P-uptake. • High nitrite inhibited the potential of carbon utilization and glycogen synthesis. Denitrifying phosphorus removal using nitrite as an electron acceptor is an innovative, resource-efficient approach for nitrogen and phosphorus removal. However, the inhibitory effects of nitrite on anoxic phosphorus uptake and process stability are unclear. This study investigated the total phosphorus removal performance under nitrite stress and analyzed microbiome responses in 186 sludge samples. The results indicated that the total phosphorus removal rates and dominant taxon abundance were highly similar under nitrite stress. High nitrite stress induced a community-state shift, leading to unstable dynamics and decreased total phosphorus removal. This shift resulted from increased species cooperation. Notably, the shared genera OLB8 and Zoogloea under non-inhibitory nitrite stress, suggesting their vital roles in mitigating nitrite stress by enhancing carbon and energy metabolism. The response patterns of these bacterial communities to high nitrite stress can guide the design and optimization of high-nitrogen wastewater reactors. [ABSTRACT FROM AUTHOR]