Functional Annotation Of Prokaryotic Taxa Research Articles

Soil organic carbon, pH, and ammonium nitrogen controlled changes in bacterial community structure and functional groups after forest conversion

IntroductionLand-use changes significantly impact soil properties in forests, which is an area of concern. Therefore, the effects of changing forest types on soil microbial communities and their functions in northern subtropical forest regions need to be further researched.MethodsWe used 16S rDNA sequencing and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to assess the variation of soil bacterial communities and potential functions related to carbon (C) and nitrogen (N) cycling in two soil layers (0–10 and 10–30 cm) after the conversion of the secondary masson pine (Pinus massoniana, PM) forest to plantations of slash pine (Pinus elliottii, PE) and Chinese fir (Cunninghamia lanceolata, CL) located in Jingde County, Anhui Province, China.ResultsThe study found that converting coniferous secondary forests to coniferous plantations resulted in a notable increase in soil pH and a decrease in nitrate nitrogen and organic carbon contents. Additionally, soil microbial diversity increased significantly, and microbial community structure changed, particularly in the topsoil. These changes might affect the C- and N-cycling mediated by soil bacteria. The analysis revealed a significant decrease in the abundance of functional groups associated with C-cycling and a significant increase in the abundance of functional groups associated with N-cycling, particularly those associated with denitrification. Soil organic carbon, pH, and ammonium nitrogen were the most critical variables affecting changes in the soil microbial community.DiscussionThese findings provide valuable information for ecological restoration and future sustainable forest management.

Soil bacterial community structure and co‐occurrence networks in response to the succession of secondary forests in subtropical regions

AbstractA large amount of secondary successional vegetation (subtropical evergreen broadleaved forests) has formed after the extensive deforestation and cultivation of coniferous forests in Wuyi Mountain, Southeast China. However, we lack a detailed understanding of the dynamic changes in microbial community structure and its co‐occurrence network during succession. The features that are responsible for alterations in the soil bacterial community remain poorly defined. Therefore, we compared the soil physicochemical properties, enzyme activities, and bacterial diversity among three different forests (a coniferous forest [CF], early stage of succession; a mixed conifer‐broadleaf forest [CBMF], middle stage of succession; an evergreen broadleaf forest [EBF]; late stage of succession). Results indicated that the contents of soil organic carbon and microbial biomass carbon (MBC) in CBMF were higher compared with those in CF. The alpha diversity indices were the highest in CBMF. Functional annotation of prokaryotic taxa predicted the relative abundances of chemoheterotrophy and aerobic chemoheterotrophy were lower in CF than in the other two forests. Bacterial network topology was affected by forest succession, with CBMF having more complex bacterial networks. Mantel's test indicated the soil nitrate nitrogen content (P = 0.03) was the most important property that shaped the bacterial community composition, bacterial diversity was influenced by soil pH (P = 0.026), and the contents of available phosphorus (P = 0.04) and MBC (P = 0.022) during the succession process. In conclusion, the succession of secondary forests promoted soil nutrient accumulation and improved bacterial diversity and network complexity.

Mature compost promotes biodegradable plastic degradation and reduces greenhouse gas emission during food waste composting

Mature compost can promote the transformation of organic matter (OM) and reduce the emission of polluting gases during composting, which provides a viable approach to reduce the environmental impacts of biodegradable plastics (BPs). This study investigated the impact of mature compost on polybutylene adipate terephthalate (PBAT) degradation, greenhouse gas (GHG) emission, and microbial community structure during composting under two treatments with mature compost (MC) and without (CK). Under MC, visible plastic rupture was advanced from day 14 to day 10, and a more pronounced rupture was observed at the end of composting. Compared with CK, the degradation rate of PBAT in MC was increased by 4.44 % during 21 days of composting. Thermobifida, Ureibacillus, and Bacillus, as indicator species under MC treatment, played an important role in PBAT decomposition. Mature compost reduced the total global warming potential (GWP) by 25.91 % via inhibiting the activity of bacteria related to the production of CH4 and N2O. Functional Annotation of Prokaryotic Taxa (FAPROTAX) further revealed that mature compost addition increased relative abundance of bacteria related to multiple carbon (C) cycle functions such as methylotrophy, hydrocarbon degradation and cellulolysis, inhibited nitrite denitrification and denitrification, thus alleviating the emission of GHGs. Overall, mature compost, as an effective additive, exhibits great potential to simultaneously mitigate BP and GHG secondary pollution in co-composting of food waste and PBAT.

MyD88 exacerbates inflammation-induced bone loss by modulating dynamic equilibrium between Th17/Treg cells and subgingival microbiota dysbiosis.

This study aimed to investigate the contribution of myeloid differentiation primary-response gene 88 (MyD88) on the differentiation of T helper type 17 (Th17) and regulatory T (Treg) cells and the emerging subgingival microbiota dysbiosis in Porphyromonas gingivalis-induced experimental periodontitis. Alveolar bone loss, infiltrated inflammatory cells, immunostained cells for tartrate-resistant acid phosphatase (TRAP), the receptor activator of nuclear factor-kB ligand (RANKL), and osteoprotegerin (OPG) were quantified by microcomputerized tomography and histological staining between age- and sex-matched homozygous littermates (wild-type [WT, Myd88+/+] and Myd88-/- on C57BL/6 background). The frequencies of Th17 and Treg cells in cervical lymph nodes (CLNs) and spleen were determined by flow cytometry. Cytokine expression in gingival tissues, CLNs, and spleens were studied by quantitative polymerase chain reaction (qPCR). Analysis of the composition of the subgingival microbiome and functional annotation of prokaryotic taxa (FAPROTAX) analysis were performed. P. gingivalis-infected Myd88-/- mice showed alleviated bone loss, TRAP+ osteoclasts, and RANKL/OPG ratio compared to WT mice. A significantly higher percentage of Foxp3+CD4+ T cells in infected Myd88-/- CLNs and a higher frequency of RORγt+CD4+ T cells in infected WT mice was noted. Increased IL-10 and IL-17a expressions in gingival tissue at D14-D28 then declined in WT mice, whereas an opposite pattern was observed in Myd88-/- mice. The Myd88-/- mice exhibited characteristic increases in gram-positive species and species having probiotic properties, while gram-negative, anaerobic species were noted in WT mice. FAPROTAX analysis revealed increased aerobic chemoheterotrophy in Myd88-/- mice, whereas anaerobic chemoheterotrophy was noted in WT mice after P. gingivalis infection. MyD88 plays an important role in inflammation-induced bone loss by modulating the dynamic equilibrium between Th17/Treg cells and dysbiosis in P. gingivalis-induced experimental periodontitis.

Seasonal variation and human impacts of the river biofilm bacterial communities in the Shiting River in southeastern China.

Bacterial communities in epilithic biofilm plays an important role in biogeochemistry processes in freshwater ecosystems. Nevertheless, our understanding of the geographical and seasonal variations of the composition of bacterial communities in the biofilm of gravels on river bed is still limited. Various anthropogenic activities also influence the biofilm bacteria in gravel rivers. By taking the Shiting River in the upper Yangtze River basinin Sichuan Province as an example, we studied the geographical and seasonal variations of epilithic bacteria and the impacts of weirs and other human activities (e.g., sewage pollution). The river has experienced severe degradation since the Ms 8.0 Wenchuan Earthquake, and weirs were constructed to prevent bed erosion.We collected epilithic biofilms samples at 17 sites along ~ 30km river reach of the Shiting River in the autumn of 2021 and the summer of 2022, respectively. We applied 16S rRNA gene high-throughput sequencing technology and Functional Annotation of Prokaryotic Taxa (FAPROTAX) to analyze the seasonal and biogeographic patterns and potential functions of the biofilm bacterial communities. The results showed that epilithic bacteria from the two surveys exhibited variation in community composition, bacterial diversity and potential functions. The bacteria samples collected in the autumn have much higher alpha diversity and richness than those collected in the summer. Bacterial richness and diversity were lower downstream of the weirs than upstream. Low diversity was observed at a sampling site influenced by sewage inflow, which contains high level of nitrogen-related chemicals.

Difference in composition and functional analysis of bacterial communities between Mytilus galloprovincialis gills and surrounding water in a brackish inshore bay, analyzed by 16S rDNA multi-amplicon sequencing

BackgroundLagoons are important natural systems, with attractive favorable conditions for aquaculture production, such as shellfish cultivation. Despite their socio-economic relevance for human activity, information on the microbial diversity, community composition, and putative functions of gill-associated microbiota and seawater is still limited, particularly as regards the extent of specific taxa enrichment within the gills and the relative effects of the temporal and spatial variables. In this study, we used a 16S rDNA multi-amplicon sequencing approach using an Ion GeneStudio S5 System and a function prediction method (Functional Annotation of Prokaryotic Taxa (FAPROTAX), to inspect the springtime dynamics of microbial communities and their inferred metabolic features in an Adriatic lagoon (Po Delta, Italy).ResultsMussels and surrounding seawater were sampled in two rearing areas three times between April and June 2021. Sequencing results showed significant (p ≤ 0.05) differences in bacterial community composition and diversity between gills and seawater. Gills were dominated by the Methylobacterium-Methylorubrum and Burkholderia-Caballeronia-Paraburkholderia genera, while in seawater samples Izamaplasma, Planktomarina, and Candidatus Aquiluna were detected as being dominant. The microbiota composition did not differ significantly between the two rearing areas. The sampling time, although limited to a 3-month timeframe, instead revealed a structural variation of the bacterial profile both in gills and seawater for alpha and beta diversities respectively. The functional prediction analysis highlighted an overexpression of human gut-associated bacteria in relation to the season-related increase in seawater temperature.ConclusionsThese findings enhance our understanding of the differences between gill-associated and seawater microbiota composition and provide novel insights into the functions carried out by bacteria inhabiting these niches, as well as on the key host-symbiont relationships of bivalves in lagoon environments.

Differential Responses of Bacterial Communities in Rhizosphere and Bulk Soils of Cotton to Long-Term Amelioration Practices Based on Freezing Saline Water Irrigation and Plastic Mulching in a Coastal Saline Soil

Soil amelioration in coastal saline areas plays an important role in alleviating land resource shortages, improving regional ecological environments, ensuring food security, and promoting economic development. Plastic mulching (M) and the combination of freezing saline water irrigation and plastic mulching (WIM) are successful amelioration practices that dramatically reduce the salinity of surface soil and facilitate plant growth in coastal saline soil. However, the bacterial responses that are closely related to these amelioration practices in coastal saline soil remain poorly understood. In this study, bacterial richness and diversity, community composition, and potential ecological functions in the rhizosphere and bulk soils of cotton in M and WIM treatments, along with a control treatment, were investigated using high-throughput sequencing in a coastal saline field. The results showed that both the M and WIM treatments increased bacterial richness and alpha diversity, which were in general significantly higher in bulk soil than in rhizosphere soil. Non-metric multidimensional scaling and the Bray–Curtis dissimilarity analysis revealed that the bacterial community in rhizosphere soil was assembled far from those in the control and bulk soils and behaved more specifically in rhizosphere soil than in bulk soil. The relative abundances of most of the dominant phyla showed opposite trends of variation in bulk and rhizosphere soils compared to those in control soil in both M and WIM treatments; in particular, the specific bacterial groups of Proteobacteria and Actinobacteria decreased in bulk soil but significantly increased in rhizosphere soil. Functional groups of chemoheterotrophy, aerobic chemoheterotrophy, and nitrate reduction were predominant in rhizosphere rather than bulk soil, according to the Functional Annotation of Prokaryotic Taxa. These findings improve the understanding of the mechanism of bacterial responses to amelioration practices M and WIM in coastal saline soils and provide valuable information for the development of amelioration techniques based on agricultural practices and soil microbiome to enhance plants’ adaptability to saline soil in the future.

Effects of the polyhalogenated carbazoles 3-bromocarbazole and 1,3,6,8-tetrabromocarbazole on soil microbial communities

Soil ecosystems are being more contaminated with polyhalogenated carbazoles (PHCZs), which raising much attention about their impact on soil microorganisms. 3-Bromocarbazole (3-BCZ) and 1,3,6,8-tetrabromocarbazole (1,3,6,8-TBCZ) are two typical PHCZs with high detection rates in the soil environment. However, ecological risk research on these two PHCZs in soil is still lacking. In the present study, after 80 days of exposure, the ecological influence of 3-BCZ and 1,3,6,8-TBCZ was investigated based on 16S rDNA sequencing, ITS sequencing, gene (16S rDNA, ITS, amoA, nifH, narG and cbbL) abundance and soil enzyme activity. The results showed that the bacterial 16S rDNA gene abundance significantly decreased under 3-BCZ and 1,3,6,8-TBCZ exposure after 80 days of incubation. The fungal ITS gene abundance significantly decreased under 1,3,6,8-TBCZ (10 mg/kg) exposure. PHCZs contributed to the alteration of bacteria and fungi community abundance. Bacteria Sphingomonas, RB41 and fungus Mortierella, Cercophora were identified as the most dominant genera. The two PHCZs consistently decreased the relative abundance of Sphingomonas, Lysobacter, Dokdonella, Mortierella and Cercophora etc at 80th day. These keystone taxa are related to the degradation of organic compounds, carbon metabolism, and nitrogen metabolism and may thus have influence on soil ecological functions. Bacterial and fungal functions were estimated using functional annotation of prokaryotic taxa (FAPROTAX) and fungi functional guild (FUNGuild), respectively. The nitrogen and carbon metabolism pathway were affected by 3-BCZ and 1,3,6,8-TBCZ. The soil nitrogen-related functions of aerobic ammonia oxidation were decreased but the soil carbon-related functions of methanol oxidation, fermentation, and hydrocarbon degradation were increased at 80th day. The effects of 3-BCZ and 1,3,6,8-TBCZ on the abundances of the amoA, nifH, narG, and cbbL genes showed a negative trend. These results elucidate the ecological effects of PHCZs and extend our knowledge on the structure and function of soil microorganisms in PHCZ-contaminated ecosystems.

Gut microbiome variation based on 16S rRNA gene amplicon sequencing of the wild and domesticated broodstock populations of black tiger shrimp (Penaeus monodon) in the Indo-Pacific region

Gut microbiome variation has functional importance on host fitness, ecology, and evolution, but the scope and basis of microbial diversity for marine shrimp are still not fully understood. The aim of present study is to characterize the gut microbiomes of five Penaeus monodon broodstocks populations of wild and aquaculture environments within the Indo-Pacific region. We conducted data analysis of 16S rRNA gene amplicons using Qiime2 and Microbiomeanalyst and functional prediction by FAPROTAX (Functional Annotation of Prokaryotic Taxa). Our results identified considerable variation in the gut microbiomes of wild and cultured shrimps, presumably reflecting differences in diet, host genetic divergence, and host-bacteria co-evolution. While wild shrimp broodstocks had higher gut microbial diversity, a pronounced divergence of core microbiota was detected in PCOA analysis for both wild and cultured shrimp populations with altered community structure and predicted metabolic functions. Proteobacteria was observed to be dominated in the gut microbiome in all P. monodon populations, whereas Gracilibacteria and Fusobacteriia were only found in domesticated populations. Interestingly, probiotic bacteria such as genus Enterococcus and Lactobacillus were observed to be the core genus for both wild populations with range from 1.08% to 17.67%. LEfSe analysis detected significant enrichment of beneficial/opportunistic pathogens from the gut microbiome of each host population, suggesting possible biomarkers for host health monitoring. Our results provide insights into the deterministic factors contributing to the interpopulation variation in the P. monodon microbiome, highlighting potential future research directions in areas such as host-bacteria co-evolution and holobiome, which may enable the assessment of host-species genomic divergence across environmental gradients.

Effects of Pine Wilt Disease on Rhizosphere Microbiota and Fine Root Fungi: Insights into Enzyme Activity, Ectomycorrhizal Infection and Microbial Composition

Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, poses a severe threat to pine forests worldwide. However, the understanding of the impact of PWD on the host microbiome remains limited. This study aimed to investigate the structure and function of the fungal community associated with Pinus thunbergii fine roots and the rhizosphere fungi and bacteria of the tree naturally infected by PWN and the healthy tree. We employed high-throughput sequencing in conjunction with functional prediction tools (Functional Annotation of Prokaryotic Taxa and Fungi Functional Guild) and soil enzyme activity measurements between the two treatments (disease vs. health). The results showed that PWD significantly decreased the activity of β-cellobiosidase (CEL) and β-glucosidase (GLS) enzymes involved in carbon cycling in the rhizosphere (p < 0.05). However, PWD did not alter the diversity of rhizosphere bacteria and fine root fungi, but it did cause a significant decrease in the richness of rhizosphere fungi (p < 0.05). Moreover, PWD significantly reduced the abundance of Actinobacteria and genus Gaiella (p < 0.05). Functionally, bacterial intracellular parasites exhibited a higher abundance in the rhizosphere after PWN infection, whereas ureolysis showed a lower abundance (p < 0.05). Fungal saprotroph–symbiotroph exhibited a higher abundance in the rhizosphere after PWN infection, whereas symbiotroph showed a lower abundance (p < 0.05). Additionally, it led to a significant reduction in the infection rate of ectomycorrhizal fungi (p < 0.05). Infected host fine root exhibited higher abundance of pathotroph–symbiotroph, whereas symbiotroph had a lower abundance (p < 0.05). These findings provided valuable insights into the interactions between pine wilt disease, plant microbial communities, and soil enzyme activity.

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants

The development of industrial parks has become an important global trend contributing significantly to economic and industrial growth. However, this growth comes at a cost, as the treatment of multisource industrial wastewater generated in these parks can be difficult owing to its complex composition. Microorganisms play a critical role in pollutant removal during industrial park wastewater treatment. Therefore, our study focused on the microbial communities in five full-scale industrial park wastewater treatment plants (WWTPs) with similar treatment processes and capacities. The results showed that denitrifying bacteria were dominant in almost every process section of all the plants, with heterotrophic denitrification being the main pathway. Moreover, autotrophic sulfur denitrification and methane oxidation denitrification may contribute to total nitrogen (TN) removal. In plants where the influent had low levels of COD and TN, dominant bacteria included oligotrophic microorganisms like Prosthecobacter (2.88 % ~ 10.02 %) and hgcI_clade (2.05 % ~ 9.49 %). Heavy metal metabolizing microorganisms, such as Norank_f__PHOS-HE36 (3.96 % ~ 5.36 %) and Sediminibacterium (1.86 % ~ 5.34 %), were prevalent in oxidation ditch and secondary settling tanks in certain plants. Functional Annotation of Prokaryotic Taxa (FAPROTAX) revealed that microbial communities in the regulation and hydrolysis tanks exhibited higher potential activity in the nitrogen (N) and sulfur (S) cycles than those in the oxidation ditch. Sulfate/sulfite reduction was common in most plants, whereas the potential occurrence of sulfide compounds and thiosulfate oxidation tended to be higher in plants with a relatively high sulfate concentration and low COD content in their influent. Our study provides a new understanding of the microbial community in full-scale industrial park WWTPs and highlights the critical role of microorganisms in the treatment of industrial wastewater.

Coupling and decoupling of marine stramenopiles and cyanobacteria in eutrophic coastal waters of Korea

The spatiotemporal distribution of MASTs (MArine STramenopiles), mostly affiliated with heterotrophic protists, and their interactions with Synechococcales were investigated in an anthropogenically polluted bay of the East Sea using 18S rRNA and 16S rRNA gene sequences. The bay was characterized by strong stratification between the surface and bottom layers and cold and nutrient-rich water intrusion in summer, whereas the bay water was well mixed in winter. MAST-3, MAST-6, MAST-7, and MAST-9 were the major MAST clades, whereas the dominance of MAST-9 declined from >80 % in summer to <10 % in winter and the diversity of MAST communities increased in winter. Co-occurrence network analysis via the sparse partial least squares revealed that MAST-3 had a Synechococcales-specific interaction during the study periods but prey-specific interactions with other MAST clades were not detected. Temperature and salinity markedly influenced the relative abundance of major MAST clades. The relative abundance of MAST-3 increased at temperatures above 20 °C and salinities above 33 ‰, however, the abundance of MAST-9 decreased under the same conditions. Analysis of the metabolic functions of cyanobacteria using the FAPROTAX (Functional Annotation of Prokaryotic Taxa) indicated that the response of photosynthetic cyanobacteria to NH4+ and PO43− was significant in summer but these functions were not tightly coupled with the abundance of Synechococcales. Similarly, strong associations of MAST-3 with high temperature/salinity and Synechococcales were indicative of coupled cascading during bottom-up processes. However, other major MAST clades were likely decoupled with Synechococcales and environmental conditions in which cyanobacteria can thrive. Therefore, our results demonstrated that MAST communities can couple or decouple with environmental variables and potential prey depending on MAST clades. Collectively, our findings provide novel insights into the role of MAST communities in microbial food webs in eutrophic coastal waters.

Tropical lacustrine sediment microbial community response to an extreme El Niño event

Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015–2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

Diversity and functional roles of the symbiotic microbiome associated to marine sponges off Karah Island, Terengganu, Malaysia

Marine sponges harbor a complex microbial consortium that plays important roles in host metabolisms and the production of chemical compounds. Symbiotic microbial community structures of marine sponges have been studied in recent years especially in the Caribbean and the Mediterranean Sea, whereas there is still a paucity of research in Malaysia. This study investigated the microbial community structures associated with four different marine sponge species (Aaptos suberitoides (Brøndsted, 1934), Neopetrosia exigua (Kirkpatrick, 1900), Theonella swinhoei (Gray, 1868), and Xestospongia testudinaria (Lamarck, 1815)) collected from Karah Island, Peninsular Malaysia. Microbial genomic DNA of four sponges and surrounding seawater were extracted and 16S rRNA gene amplicon sequencing was conducted targeting V3–V4 variable region using Illumina MiSeq platform. Paired-end sequences were analyzed using QIIME2 and the potential microbial functions related to the microbial communities of marine sponges and seawater were annotated using functional annotation of prokaryotic taxa (FAPROTAX). Microbial community structures and compositions were clearly different between sponges and seawater, as well as within different sponge species. Taxonomic analysis showed that Chloroflexi was the predominant phylum in all sponge species. Proteobacteria and Actinobacteriota were composing the core taxa of the microbial communities in N. exigua, T. swinhoei, and X. testudinaria, whereas Cyanobacteria and Proteobacteria were dominant in A. suberitoides. The functional analysis revealed that the abundance of the “predatory or exoparasitic” function was high in all sponges. The functions of aerobic ammonia oxidation and nitrification were dominant in marine sponges, rather than seawater. This study has important implications in understanding the microbial community structures associated with marine sponges in Malaysia, and gives fundamental information of sponge–microbe interactions and functional roles for future investigations.

Different grazers and grazing practices alter the growth, soil properties, and rhizosphere soil bacterial communities of Medicago ruthenica in the Qinghai-Tibetan Plateau grassland

Livestock grazing is a popular land-use activity for grasslands. Over grazing and trampling of livestock impairs ecosystem function by changing vegetation growth, soil nutrients, and soil bacterial communities. However, information regarding the characteristics of those allied with above- and belowground of grazing-resistant host plant species under different grazers and grazing practices in grassland ecosystems is limited. We examined the impact of single-species grazing of yak only (YG), sheep only (SG), and mixed grazing in the ratio of yak to sheep of 1:2 (MG (1:2)), 1:4 (MG (1:4)), and 1:6 (MG (1:6)) on plant growth, soil properties, and soil microbial communities. Plant biomass and soil properties were measured in each treatment, and soil microbial communities in the rhizosphere soil of Medicago ruthenica were analyzed by high-throughput sequencing of the 16 S rRNA gene. The results showed that shoot height, root length, and plant FW (fresh weight) and DW (dry weight) of M. ruthenica under single-species grazing decreased by 5.60 %, 3.30 %, 11.34 % and 9.82 %, respectively; under mixed-species grazing decreased by 35.65 %, 29.68 %, 52.35 % and 55.60 %, respectively, compared to CK (no grazing). Mixed-species grazing decreased soil UR (urease), SC (sucrase), and ACP (acid phosphatase) activities by decreasing soil NH4+-N, increasing soil NO3−-N and soil SOC (soil organic carbon), compared to CK. Grazing further affected core phyla and genera of rhizosphere bacterial communities, such as Bacteroidota, Rubrobacter, and Gaiella under different grazers and grazing practices by altering soil properties. The interaction of soil bacteria under YG was more sensitive than that under SG, and the interaction of soil bacteria under mixed-species grazing was more sensitive than that under single-species grazing. According to Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis associated with N cycling, and the relative abundance of the rhizosphere bacteria with the functions of nitrogen respiration and nitrite denitrification under MG (1:2), MG (1:4), and MG (1:6) were increased by 40.75 %, 34.74 %, 32.31 %, 40.86 %, 36.17 %, and 48.11 %, respectively, compared to CK. This study demonstrates that the mechanism by which different grazers and grazing practices affect soil bacterial communities and associated soil properties in the rhizosphere soil of the legume forage species M. ruthenica will contribute to the understanding how beneficial microbes interact efficiently with grazing-tolerant plant species under different grazing practices.

Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells

Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were statistically significant. Among these functional groups, the function related to the generation of precursor metabolites and energy was the only one included in all four computational methods, and the sum total of the proportion was 93.54%. The metabolism of cofactor, carrier, and vitamin biosynthesis was included in the three methods, and the sum total of the proportion was 29.94%. The results suggested that the microbial communities usually contribute to energy metabolism, or the metabolism of cofactor, carrier, and vitamin biosynthesis might reveal the functional status in the anode of sediment MFCs.

Effects of salinity on the performance of bioflocs with activated sludge as inoculum

This study evaluated the feasibility of domesticating the bioflocs with activated sludge as inoculum at high salinity. By using the gradually increase salinity from 0.2 to 4.0%, the study evaluated the effectiveness of bioflocs in sustaining the water quality of aquaculture, the biofloc morphology characteristics and microbial community structure of bioflocs in order to discover the influence of salinity. From the perspective of sustaining the water quality of bioflocs, the COD removal efficiency dropped sharply from 63.9% to 3.7%, the NO3−-N was maintained below 0.5 mg/L but the NH4+-N exceeded the safety threshold of aquaculture at the salinity of 2.5–4.0%. From the pespective of flocculation of flocs, the biofloc volume index and content were maintained at about 30 ml/g and 7 g/L, while the floc particle size (45–200 um) tended to increase cumulatively, showing good agglomeration, sedimentation and stability. From the pespective of floc microbial community structure, Arenibacter, Thauera, Paracoccus and Denitromonas became the dominant genera with relative abundances of 4.8–7.5%, 4.9–17.1%, 3.0–4.7% and 5.3–14.1% at 3.0–4.0% salinity, respectively, however, the relative abundance of Candidatus Competibacter rapidly decreased from 15.0% to 2.5% with the increasing salinity from 1.0% to 4.0%. Furthermore, Redundancy analysis (RDA) indicated that salinity was a key environmental factor affecting floc community, and Functional Annotation of Prokaryotic Taxa (FAPROTAX) confirmed the promoted flocs denitrification as well as inhibited nitrification and hydrocarbon cycling in higher salinity to some extent. This study demonstrated the feasibility of using freshwater activated sludge as a base nucleus for biofloc formation for salinity up to 2% – 2.5%, which provided a useful reference for improving the taste and nutritional value of fish cultured by Biofloc Technology (BFT).

Ecological risk assessment of glyphosate and its possible effect on bacterial community in surface sediments of a typical shallow Lake, northern China

Glyphosate is a widely used herbicide worldwide and its prevalent presence in aquatic ecosystems poses a threat to living organisms. This study evaluated potential ecological risk of glyphosate to sediment-dwelling organisms and assessed the probable effect of glyphosate on structure and predicated function of sediment-attached bacterial communities from a large shallow lake in northern China based on 16S rRNA high-throughput sequencing. Results suggested that glyphosate showed a medium to high concentration (up to 8.63 mg/kg) and chronic risk to sediment-dwelling organisms (10% samples exhibiting medium to high risk quotient), especially in sites nearby farmland and residential areas in August. Bacterial community identification based on 16S rRNA sequence indicated some species of dominant phylum Proteobacteria and Campilobacterota (e.g., Steroidobacteraceae, Thiobacillus, Gallionellaceae, Sulfurimonadaceae) were stimulated while some species of dominant phylum Actinobacteriota, Acidobacteriota and Firmicutes (e.g., Nocardioidaceae, Microtrichales, Vicinamibacteraceae, Paenisporosarcina) were inhibited by glyphosate accumulation. The stimulating species were related to sulfur-oxidizing, sulfate-, iron-, or nitrate-reducing bacteria; The inhibiting species were related to plant bacterial endophytes, polyphosphate-accumulating organisms (PAOs) and denitrifers. Correspondingly, promoted bacterial metabolic functions of “sulfite respiration”, “nitrogen respiration”, “aromatic compound degradation” and “nitrification” but suppressed “cellulolysis”, “manganese oxidation”, “anoxygenic photoautotrophy S oxidizing” and “nitrate denitrification” were predicated on functional annotation of prokaryotic taxa. Although these results could only partly suggest the impacts of glyphosate on the bacterial communities due to the lack of actual results from control experiments, the identified Steroidobacteraceae could be thought as a bioindicator in the future mechanism study for the ecological effect and bioremediation of glyphosate. This work intends to arise the concern about the depletion of biodiversity and bacterial metabolic functions with contribution of glyphosate in part in eutrophic lakes.

Nitrogen occurrence forms and bacterial community in sediment influenced by Bellamya purificata bioturbation

Endogenous water pollution and excessive nitrogen in ponds have always been prominent problems threatening aquaculture. To solve this problem, a 70-day indoor simulation experiment was conducted. The snail Bellamya purificata was stocked at four different densities: 0, 15, 30, and 60 individuals/tank, represented as CON (control), LD (low density), MD (medium density), and HD (high density), respectively, to investigate the effects of B. purificata on the nitrogen occurrence forms and bacterial communities in the sediment. At the end of the experiment, the nitrate concentration was significantly higher, while the total nitrogen content was significantly lower in the MD group than in the other three groups. Ammonia monooxygenase activity was significantly lower in the CON group than in the other three groups, and hydroxylamine oxidase activity was significantly higher in the HD group than in the other three groups. The CON and MD groups showed the highest and lowest values in nitrate reductase activity, respectively. The hydroxylamine reductase activity decreased significantly with increasing density. Through 16S ribosomal RNA (rRNA) high-throughput sequencing, significantly affected bacterial communities by B. purificata were found. Alpha diversity results showed that, a significantly lower Shannon index was observed in the MD group than in the other three groups. The LD and MD groups showed the highest and lowest Chao1 index values, respectively. Phyla Nitrospinae and family Nitrosomonadaceae were significantly enriched in the HD and MD groups, respectively. Redundancy analysis (RDA) indicated a significant correlation between differential bacterial taxa and TN content. Predicted functional analysis based on FAPROTAX (Functional annotation of prokaryotic taxa) database showed that functional groups aerobic ammonia oxidation and aerobic nitrite oxidation were significantly enriched in the MD group. Overall, B. purificata significantly altered the bacterial community composition, increased hydroxylamine oxidase and ammonia monooxygenase activities, enhanced the bacterial nitrification process, and promoted the transformation of total nitrogen to nitrate. Moreover, B. purificata stocked at 30 and 60 individuals/tank appeared to have a significant promotion effect on the bacterial community and nitrogen occurrence forms in the sediment. Hence, co-culturing B. purificata may be a feasible and effective ecological restoration method to alleviate excess nitrogen and reduce water eutrophication.

Assessment of the rhizosphere fungi and bacteria recruited by sugarcane during smut invasion.

Whip smut is one of the most serious and widely spread sugarcane diseases. Plant-associated microbes play various roles in conferring advantages to the host plant. Understanding the microbes associated with sugarcane roots will help develop strategies for the biocontrol of smut. Therefore, the present study explored microbe-mediated sugarcane response to smut invasion via 16S rRNA and ITS metabarcoding survey of the rhizosphere soils of resistant and susceptible sugarcane varieties. The bacterial and fungal diversity in the rhizosphere soils differed between the resistant and susceptible varieties. The bacterial genera Sphingomonas, Microcoleus_Es-Yyy1400, Marmoricola, Reyranella, Promicromonospora, Iamia, Phenylobacterium, Aridibacter, Actinophytocola, and Edaphobacter and one fungal genus Cyphellophora were found associated with smut resistance in sugarcane. Detailed analysis revealed that the majority of bacteria were beneficial, including the actinomycete Marmoricola and Iamia and Reyranella with denitrification activity. Analysis of bacterial network interaction showed that three major groups interacted during smut invasion. Meanwhile, seven of these genera appeared to interact and promote each other's growth. Finally, functional annotation based on the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database predicted that the abundant bacteria are dominated by oxygenic photoautotrophy, photoautotrophy, and phototrophy functions, which may be related to smut resistance in sugarcane. The present study thus provides new insights into the dynamics of the sugarcane rhizosphere microbial community during smut invasion.