Phylogeny and Fungal Community Structures of Helotiales Associated with Sclerotial Disease of Mulberry Fruits in China.

Mulberry fruit sclerotiniose is a prevalent disease caused by the fungal species Ciboria shiraiana, C. carunculoides, and Scleromitrula shiraiana of the order Helotiales, and severely affects the production of mulberry. However, these species have only been identified using morphological and rDNA-ITS sequence analyses, and their genetic variation is unclear. To address this, morphological and two-locus (ITS and RPB2) phylogenetic analyses were conducted using culture-dependent and independent methods for 49 samples from 31 orchards across four provinces in China. Illumina MiSeq sequencing was used to assess the fungal communities obtained from fruits varying in disease severity and color from an orchard in Wuhan. Conidial suspensions of C. shiraiana and C. carunculoides isolated from diseased fruits, diseased fruits affected with hypertrophy and pellet sorosis sclerotiniose, and mycelia of Sclerotinia sclerotiorum were determined to be pathogenic to the mulberry cultivar YSD10. However, fruits inoculated with S. sclerotiorum mycelia exhibited nontypical disease symptoms, and mycelia and conidia obtained from C. carunculoides and S. shiraiana strains were not pathogenic. Maximum parsimony and Bayesian analyses using the sequences of the assessed loci indicated species variability with no evidence of geographic specialization. Metagenomic analysis revealed that the diversity of fungal communities was reduced with disease progression. Furthermore, within a single fruit, the presence of two Ciboria spp. was detected. These results provide novel insights into Ciboria spp., revealing the secondary infections caused by conidia in diseased fruits, genetic variations of the pathogens, and the occurrence of coinfection. This improved understanding of fungal pathogens will aid in developing effective disease control strategies.

Bacterial community composition of the sediment in Sayram Lake, an alpine lake in the arid northwest of China.

Sediment bacterial communities play a critical role in biogeochemical cycling in alpine lake ecosystems. However, little is known about the sediment microbial communities in these lakes. In this study, the bacterial community composition (BCC) and their relationships with environmental factors of the sediment in Sayram Lake, the largest alpine and cold-water inland lake, China was analyzed using Illumina MiSeq sequencing. In total, we obtained 618,271 high quality sequences. The results showed that the bacterial communities with 30 phyla and 546 genera, were spread out among the 5 furface sediment samples, respectively. The communities were dominated by Proteobacteria, Acidobacteria, Planctomycetes, Gemmatimonadetes, Chloroflexi, Actinobacteria, Verrucomicrobia and Bacteroidetes, accounting for 48.15 ± 8.10%, 11.23 ± 3.10%, 8.42 ± 2.15%, 8.37 ± 2.26%, 7.40 ± 3.05%, 5.62 ± 1.25%, 4.18 ± 2.12% and 2.24 ± 1.10% of the total reads, respectively. At the genus level, the communities were dominated by Aquabacterium, Pseudomonas, Woeseia, MND1, Ignavibacterium and Truepera, accounting for 7.89% ± 8.24%, 2.32% ± 1.05%, 2.14% ± 0.94%, 2% ± 1.22%, 0.94% ± 0.14% and 0.80% ± 0.14% of the total reads, respectively. Statistical analyses showed the similarity of the sediment bacterial communities at our field sites was considerably low, far below 35%, and total organic carbon (TOC) was the dominant environmental factor affecting the spatial changes of BCC in the sediment. Thus, this study greatly improving our understanding of the microbial ecology of alpine lake in the arid and semi-arid ecosystems today so seriously threatened.

Effects of different seasons on bacterial community structure in rose rhizosphere soil.

TO explore the changes of rhizosphere soil bacterial community of Rosa rugosa "Fenghua", Rosa rugosa cv. Plena and Rosa rugosa "Zizhi" in different seasons, the Illumina Miseq sequencing and the correlation network analysis of dominant flora was used. The results showed that the bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria, with Sphingomonas, GP6, GP4, Novosphingobium, Wps-1_genera_incertae_sedis, and Massilia as the dominant genera. The correlation network analysis showed that, as the dominant group with the highest relative abundance, Sphingomonas had a significant positive correlation with Gemmatimonas, Aridibacter, GP3, GP4, and Flavisolibacter, and a significant negative correlation with Solirubrobacter, indicating that it could work synergistically with a variety of microorganisms to contribute to soil metabolism and the growth and development of roses. The results revealed the diversity of microbial structures in the rhizosphere soil of Rosa rugosa "Fenghua", Rosa rugosa cv. Plena and Rosa rugosa "Zizhi", and this will provide a theoretical basis for exploring the change rules of microbial communities, screening and utilizing beneficial microorganisms, and maintaining the growth and development of roses. KEY POINTS: • Variations from season to season significantly affected the bacterial community structure. • There was less variability in the bacterial community structure between rose varieties. • Sphingomonas was the dominant bacterium in all seasons.

Diversity of bacterium communities in saline-alkali soil in arid regions of Northwest China.

BACKGROUND: The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources. RESULTS: The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks. CONCLUSIONS: The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).

Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China.

Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.

Effect of pyrene and phenanthrene in shaping bacterial communities in seagrass meadows sediments.

Polycyclic aromatic hydrocarbons (PAHs), originating from anthropogenic and natural sources, are highly concerned environmental pollutants. This study investigated the impact of two model PAHs (pyrene and phenanthrene) on bacterial community succession in the seagrass meadows sediment in a lab-scale microcosm. Halophila ovalis sediment slurry microcosms were established, one group was placed as a control, and the other two were treated with pyrene and phenanthrene. Bacterial community succession in response to respective PAHs was investigated by 16S rRNA amplicon sequencing. The results demonstrated that bacterial diversity decrease in each microcosm during the incubation process; however, the composition of bacterial communities in each microcosm was significantly different. Proteobacteria (37-89%), Firmicutes (9-41%), and Bacteroides (7-21%) were the predominant group at the phylum levels. Their abundance varies during the incubation process. Several previously reported hydrocarbon-degrading genera, such as Pseudomonas, Spinghobium, Sphingobacterium, Mycobacterium, Pseudoxanthomonas, Idiomarina, Stenotrophomonas, were detected in higher abundance in pyrene- and phenanthrene-treated microcosms. However, these genera were distinctly distributed in the pyrene and phenanthrene treatments, suggesting that certain bacterial groups favorably degrade different PAHs. Statistical analyses, such as ANOSIM and PERMANOVA, also revealed that significant differences existed among the treatments' bacterial consortia (P < 0.05). This work showed that polycyclic aromatic hydrocarbon significantly affects bacterial community succession, and different PAHs might influence the bacterial community succession differently.

Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.

Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.

Metagenomic analysis of microbial community succession during the pickling process of Zhacai (preserved mustard tuber) and its correlation with Zhacai biochemical indices.

BACKGROUND: Industrial Fuling Zhacai is pickled by a method summarized as 'three times pickled and pressed', in which raw mustard tubers are subjected to three stages of pickling in different salt concentrations, with a pressing operation at the end of each stage to remove brine. This study used Illumina MiSeq technology and multivariate statistical analyses to investigate microbial community succession during the pickling process and its correlation with Zhacai biochemical indices. RESULTS: A total of 19 phyla, 208 genera, and 295 species of bacteria were identified. Lactobacillus was the dominant genus of bacteria in all three stages and Lactobacillus sakei was the dominant species in the first and second stages. A total of six phyla, 200 genera and 301 species of fungi were also identified. According to a PICRUSt2 prediction, the main functions of the bacterial and fungal communities were carbohydrate and protein metabolism, while alcohol metabolism was also a function of fungi. Nine bacterial genera closely correlated with Zhacai biochemical indices: Acinetobacter, Pseudomonas, Pedobacter, Erwinia, Lactobacillus, Chryseobacterium, Flavobacterium, Duganella, and Paenarthrobacter. Six genera of fungi correlated closely: Penicillium, Cystobasidium, Cladosporium, Plenodomus, Aspergillus, and Simplicillium. All these genera probably originated from the surface microorganisms of raw mustard tuber. CONCLUSION: This study reveals the succession patterns of microbial community structures during the pickling process of industrial Zhacai and infers the core functional flora, providing reference data for Zhacai pickling process control. © 2020 Society of Chemical Industry.

Long-term agricultural contamination shaped diversity response of sediment microbiome.

The pollution caused by agricultural production poses a threat to the ecological integrity of river ecosystems, altering the structure and function of river ecosystems. Differences in microbial community structure provide useful information about the impact of agricultural pollution on the biological integrity of ecosystems, but generally convey little information regarding ecosystem functions. In this study, using Illumina MiSeq sequencing technology based on the 16S rRNA gene, river sediment samples associated with four different types of agricultural pollution were comprehensively analyzed. The results show that the total organic carbon (TOC) content was highest at the YZS site (animal husbandry sewage) among the assayed sites, but the species richness and uniformity were lowest at this site, which may have been caused by the high nutrient source of the sewage. Furthermore, in the three YZS samples affected by the long-term discharge of aquaculture tail-water, the unique genus Dechloromonas and the genus Candidatus-Competitor were observed, which are strongly correlated with phosphorus conversion. The formation of network modules may correspond to the coexistence of functional bacteria accustomed to multiple niche combinations under different agricultural pollution conditions in river sediments. According to the PICRUSt functional prediction, the bacterial community in the agricultural polluted river sediment primarily harbored 46 subfunctions, exhibiting richness of functions. Overall, our results provide a more comprehensive understanding of the structure and ecological processes associated with the aggregation of bacterial communities, which is beneficial for the management of river environments.

Bacterial Community Structure and Diversity in the Aqueous Environment of Shihou Lake and its Relationship with Environmental Factors.

Microorganisms are sensitive to changes in the external environment and are often used as indicators to monitor and reflect water quality. Using Illumina MiSeq sequencing, the characteristics of the microbial community in Shihou Lake water at different time points were analyzed and the key environmental factors affecting the bacterial community were identified. The microbial community diversity in Shihou Lake water was rich and showed significant differences over time. The main bacterial phyla were the Cyanobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi, Planctomycetes, Firmicutes, Chlorobi, WS6 and Saccharibacteria. The relative abundance of these major phyla in the sample accounted for 97.83%-99.07% of the total abundance; Cyanobacteria had the highest relative abundance, accounting for 13.07%-44.61% of the total, and the abundance of each dominant phylum was significantly different at different time points. The Shannon and Simpson indexes showed that the diversity of each month was as follows: August > October > July > September > November. The Chao1 and Ace indexes indicated that the order of richness was: November > October > July > August > September. Beta diversity analysis found significant differences in the samples from month to month. Environmental factors such as temperature, total nitrogen, chlorophyll-a, permanganate index, nitrite, pH and ammonia nitrogen had significant effects on microbial community structure.

Long-term effects of mixed planting on arbuscular mycorrhizal fungal communities in the roots and soils of Juglans mandshurica plantations.

BACKGROUND: Establishing mixed plantations is an effective way to improve soil fertility and increase forest productivity. Arbuscular mycorrhizal (AM) fungi are obligate symbiotic fungi that can promote mineral nutrient absorption and regulate intraspecific and interspecific competition in plants. However, the effects of mixed plantations on the community structure and abundance of AM fungi are still unclear. Illumina MiSeq sequencing was used to investigate the AM fungal community in the roots and soils of pure and mixed plantations (Juglans mandshurica × Larix gmelinii). The objective of this study is to compare the differential responses of the root and rhizosphere soil AM fungal communities of Juglans mandshurica to long-term mixed plantation management. RESULTS: Glomus and Paraglomus were the dominant genera in the root samples, accounting for more than 80% of the sequences. Compared with that in the pure plantation, the relative abundance of Glomus was higher in the mixed plantation. Glomus, Diversispora and Paraglomus accounted for more than 85% of the sequences in the soil samples. The relative abundances of Diversispora and an unidentified genus of Glomeromycetes were higher and lower in the pure plantation, respectively. The Root_P samples (the roots in the pure plantation) had the highest number of unique OTUs (operational taxonomic units), which belonged mainly to an unidentified genus of Glomeromycetes, Paraglomus, Glomus and Acaulospora. The number of unique OTUs detected in the soil was lower than that in the roots. In both the root and soil samples, the forest type did not have a significant effect on AM fungal diversity, but the Sobs value and the Shannon, Chao1 and Ace indices of AM fungi in the roots were significantly higher than those in the soil. CONCLUSIONS: Mixed forest management had little effect on the AM fungal community of Juglans mandshurica roots and significantly changed the community composition of the soil AM fungi, but not the diversity.

Analysis of endophytic and rhizosphere bacterial diversity and function in the endangered plant Paeonia ludlowii.

Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii. Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii. This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.

Metagenomic analysis of soil microbial community under PFOA and PFOS stress.

Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.

Impact of dichlorprop on soil microbial community structure and diversity during its enantioselective biodegradation in agricultural soils.

Enantioselective biodegradation of racemic dichlorprop in two soils was investigated in the laboratory. Chiral separation of racemic dichlorprop was achieved by using HPLC with Phenomenex Lux Amylose-2. The first-order kinetic model fitted well the dissipation data of racemic dichlorprop and its pure R- and S-enantiomers. S-dichlorprop was preferentially degraded in both soils and enantioselectivity was affected by soil pH. The half-lives (DT50) of S-dichlorprop were 8.22 days in soil A and 8.06 days in soil D, while R-dichlorprop was more persistent with DT50 of 12.93 days in soil A and 12.38 days in soil D, respectively. Dichlorprop dissipated faster in soil D with lower organic matter content. In sterilized soils, neglected dissipation was observed and enantiomer fraction values remained constant, indicating that the enantioselective degradation was mainly controlled by soil microorganisms. Soil microbial community structure and diversity was assessed by Illumina MiSeq sequencing of 16S rRNA genes from dichlorprop and no dichlorprop contaminated microcosms. Compared with controls, dichlorprop application had no significant effect on microbial community structures at phylum level, but increased bacterial diversity and dichlorprop degradation related taxa in both soils. S-dichlorprop preferential degradation might be attributed to the S-enantiomer preferred degraders in the family of Sphingomonadaceae.

Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity.

OBJECTIVE: This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions. METHODS: A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment. RESULTS: i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens. CONCLUSION: The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China.

BACKGROUND: Scylla paramamosain is a commercially important mud crab. The microbiota is a community that inhabits the crab intestine, and is important for physiological functional and host health. RESULTS: Proteobacteria, Firmicutes, Bacteroidetes, Tenericutes, Spirochaetae and Fusobacteria were the dominant phyla of the 36 representative phyla. Eleven genera of the 820 representative genera were considered as core gut microbiota and were distributed in the five dominant phyla. The core genus of the Proteobacteria included Arcobacter, Photobacterium, Vibrio, Shewanella and Desulfovibrio. The other four phyla contained one or two genera. Male and female crab samples had two different core genera, (male samples: Psychrilyobacter & Lactococcus; female samples: Clostridium_sensu_stricto_11 and Candidatus_Bacilloplasma). CONCLUSIONS: This is the first time core intestinal microbiota have been identified in crab from nine coastal regions of southern China. This study provides sequencing data related to the gut microbiota of S. paramamosain, and may contribute to probiotic development for S. paramamosain aquaculture industries.

The rhizomicrobiomes of wild and cultivated crops react differently to fungicides.

The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops.

Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard).

The Arctic region has been the focus of increasing attention as an ecosystem that is highly sensitive to changes associated with global warming. Although it was assumed to be vulnerable to changes in climate, a limited number of studies have been conducted on the surface sediment bacteria of Arctic fjorden. This study assessed the diversity and distribution pattern of bacterial communities in eight marine sediments along the seafloor in a high Arctic fjorden (Kongsfjorden, Svalbard). A total of 822 operational taxonomic units (OTUs) were identified by Illumina MiSeq sequencing, targeting the V3-V4 hypervariable regions of the 16S rRNA gene. In these surface marine sediments, more than half of the sequences belonged to the phylum Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi and Lentisphaerae. The bacterial genera Marinicella, Desulfobulbus, Lutimonas, Sulfurovum and clade SEEP-SRB4 were dominant in all samples. Analysis of similarity indicated that bacterial communities were significantly different among the inner, central and outer basins (r2 = 0.5, P = 0.03 < 0.05). Canonical correspondence analysis and permutation tests revealed that location depth (r2 = 0.87, P < 0.01), temperature (r2 = 0.88, P < 0.01) and salinity (r2 = 0.88, P < 0.05) were the most significant factors that correlated with the bacterial communities in the sediments. 28 differentially abundant taxonomic clades in the inner and outer basin with an LDA score higher than 2.0 were found by the LEfSe method. The Spearman correlation heat map revealed different degrees of correlation between most major OTUs and environmental factors, while some clades have an inverse correlation with environmental factors. The spatial patterns of bacterial communities along the Kongsfjorden may offer insight into the ecological responses of prokaryotes to climate change in the Arctic ecosystem, which makes it necessary to continue with monitoring.

Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol.

Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.

Mudflat reclamation causes change in the composition of fungal communities under long-term rice cultivation.

Fungi play a critical role in farmland ecosystems, especially in improving soil fertility; however, little is known about the changes in fungal communities caused by mudflat reclamation under rice cultivation. In this study, mudflats located in Yancheng, China, which were divided into nine plots with 0, 11, and 20 years of successive rice cultivation histories, were sampled to determine the fungal community composition by using Illumina MiSeq sequencing. Results show that the Shannon diversity of the fungal communities did not change significantly but the species richness increased under mudflat reclamation with long-term rice cultivation. Ascomycota was the dominant phylum throughout the reclaimed mudflats samples, while Sordariomycetes was the dominant class. Fungal functional prediction found that the relative abundance of saprotrophs gradually increased with mudflat reclamation and mainly belonged to Ascomycota after 20 years of successive reclamation. Redundancy analysis showed that electrical conductivity, organic matter, and total nitrogen were the main factors affecting the composition and ecological function of the fungal community during mudflat reclamation. In short, a fungal community dominated by Ascomycota was established during mudflat reclamation under rice cultivation, which is more conducive to promoting soil fertility because of the higher proportion of saprotrophic fungi in Ascomycota.