Bacterial Diversity Indices Research Articles

Grassland irrigation and grazing prohibition have significantly affected vegetation and microbial diversity by changing soil temperature and moisture, evidences from a 6 years experiment of typical temperate grassland

Grasslands are characterized by high primary productivity and offer a diverse array of ecosystem services that contribute to human well-being. The dynamic balance between vegetation-soil in grassland ecosystems is being affected by anthropogenic activities and climate change, in which soil microbial communities play a critical regulating role. However, how microbial biodiversity interacts with vegetation-soil and responds to environmental change remains unclear. We conducted a six-year field experiment in the grasslands of Inner Mongolia to study the effects of grazing and altered precipitation on major vegetation types (or species), soil properties, and microbial community composition. The results showed that increased precipitation influenced positive associations within microbial communities, which helped to increase vegetation diversity. The biomass of Stipa.sareptana increased by 0.054 % under reduced precipitation, while it significantly increased by 2.07 % under the combination of grazing ban and reduced precipitation. Grazing prohibition had a significant negative effect on bacterial diversity and Shannon's index, but a significant positive effect on fungal diversity and abundance. Increasing precipitation had no significant effect on bacterial diversity under grazing conditions, while decreasing precipitation significantly reduced the Shannon index of bacteria. Fungal communities were very sensitive to changes in precipitation, and both increasing and decreasing precipitation significantly affected the structure of fungal communities. In summary, our results highlight how grassland irrigation and moderate grazing can be employed as a management strategy to promote plant diversity and thereby improve ecosystem functioning and resilience.

Microbiome diversity and variations in industrial hemp genotypes

Microbes like bacteria and fungi are crucial for host plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.). Herein, we evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sensi and Cherry Wine) and two fibers (American Victory and Unknown). The four hemp varieties showed significant variations in microbiome diversity. The roots had significantly abundant fungal and bacterial endophyte diversity indices, whereas the stem had higher fungal than bacterial diversity. Interestingly, the soil system showed no significant diversity variation across CBD vs. fiber genotypes. In fungal phyla, Ascomycota and Basidiomycota were significantly more abundant in roots and stems than leaves in CBD-rich genotypes compared to fiber-rich genotypes. The highly abundant bacterial phyla were Proteobacteria, Acidobacteria, and Actinobacteria. We found 16 and 11 core-microbiome bacterial and fungal species across genotypes. Sphingomonas, Pseudomonas, and Bacillus were the core bacteria of fiber genotypes with high abundance compared to CBD genotypes. Contrarily, Microbacterium, and Rhizobium were significantly higher in CBD than fiber. The Alternaria and Gibberella formed a core-fungal microbiome of fiber-genotype than CBD. Contrarily, Penicillium, and Nigrospora were significantly more abundant in CBD than fiber genotypes. In conclusion, specific hemp genotypes recruit specialized microbial communities in the rhizosphere and phyllosphere. Utilizing the core-microbiome species can help to maintain and improve the growth of hemp plants and to target specialized traits of the genotype.

Differential study on the relationship between HPV infection and vaginal microbiota composition in Uygur and Han women

ObjectiveTo analysis the differential composition in vaginal microbial communities following HPV infection in Uygur and Han women, and to Explore the correlation between these difference and the degree of Human Papillomavirus (HPV) infection in Uygur women compared to Han women. MethodsA total of 151 Uygur and Han women, with and without HPV, were studied at Xinjiang Uygur Autonomous Region People's Hospital (June 2021–June 2022). These participants were divided into six groups: Uygur control (CV), Uygur transient infection (TPV), Uygur persistent infection (PPV), Han control (CH), Han transient infection (TPH), Han persistent infection (PPH). Vaginal microbiota diversity and dominant bacteria with or without HPV infection were compared using 16S rDNA sequencing. ResultsAfter HPV infection, vaginal pH increased significantly in Uygur and Han women. Vaginal environment cleanliness decreased notably only in Han women (P < 0.05). In Han women, Lactobacillus and Gardnerella dominated both with or without HPV infection. Prevotella, Streptococcus, and Atopobium decreased, while Sneathia increased significantly in persistent HPV cases. Among Uygur women, Gardnerella, Streptococcus, Prevotella, and Shuttleworthia increased significantly in the TPV group, with lower Lactobacillus compared to CV and PPV groups. Bacterial diversity indices (Chao1, Shannon, Simpson) were significantly lower in TPH compared to CH (P < 0.05), with no significant difference in PPH compared to CH (P > 0.05). Chao1 index was significantly lower in TPH than TPV (P < 0.05), with no difference between PPH and PPV (P > 0.05). CV group's Chao1 index was significantly lower than CH (P < 0.01). PCoA and NMDS analyses showed distinct vaginal microbiota between TPH and TPV groups. LEfSe identified 20 differentially expressed taxa in CH-TPH-PPH comparison and 17 in CV-TPV-PPV. ConclusionOur study reveals ethnic-specific differences in vaginal microbial responses to HPV infection, with notable alterations in diversity and composition. The differential patterns observed between Uygur and Han women underscore the importance of considering host ethnicity in HPV-related microbial dysbiosis, emphasizing the need for tailored interventions targeting microbial signatures to enhance HPV prevention and management strategies.

How Dryland-to-Paddy Conversion Affects the Carbon Emission Efficiency in the Short Term: Evidence from Soil Carbon-Fixing Bacteria and the Carbon Pool in an Experimental Study

To amplify grain production capacity, a global trend is emerging in which many regions are transitioning from dependence on rainfall to irrigated agriculture. An illustrative example of this form of land consolidation is the conversion from dryland to paddy fields, which has changed the ecological environment of farmlands, resulting in significant effects on carbon fixation and emissions. However, there currently exists a deficiency in essential understanding regarding the short-term effects of dryland-to-paddy conversion on ecological processes tied to soil carbon-fixation bacteria and carbon emission efficiency (CEE). Therefore, field monitoring and high-throughput sequencing were carried out to monitor the changes in soil carbon emission efficiency and carbon-fixation bacteria before and after the conversion. Our results indicate that while conversion from dryland to paddy fields can boost grain yield, it also results in an increase in soil carbon emissions and a consequent decrease of 25.78% in carbon emission efficiency. This transition has resulted in an increased soil carbon-fixing bacterial alpha diversity index and enhanced network complexity. The structural equation model indicates that changes in soil environmental factors, especially soil moisture, soil organic carbon (SOC), readily oxidizable carbon (ROC), and carbon-fixing bacteria, are the primary drivers of CEE variation (p &lt; 0.05). Given the critical role that the soil carbon cycle plays in global climate change, there is a pressing need for increased global attention towards the carbon emissions triggered by the transition from rainfed to irrigated agriculture.

Response of the Endophytic Microbiome in Cotinus coggygria Roots to Verticillium Wilt Infection.

Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of C. coggygria under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to V. dahliae infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in C. coggygria.

Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.

A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.

Straw return can increase maize yield by regulating soil bacteria and improving soil properties in arid and semi-arid areas

Straw return has been found to benefit soil fertility and crop yield, however, by which it affects microbial communities to mediate soil factors driving crop yields under maize continuous cropping systems in dryland areas is still unclear. To fill this gap, a 6-year field experiment was established with five straw return amounts (T0, T1, T2, T3, and T4, representing 0, 3000, 6000, 9000, and 12,000 kg ha−1 of straw, respectively), and investigated the effects of on soil properties, enzymes, bacterial community composition and diversity, and crop yields. Our analysis showed that soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) contents significantly increased by 1–8 %, 5–25 %, and 2–9 % under straw return treatments, respectively, compared to the T0, and soil catalase, urease, and alkaline phosphatase activities increased by at least 34.00 %. Additionally, crop yield significantly increased by 4.23–12.00 % under T1-T4 treatments, and showed highly significant relationships with SOC, TN, and TP. Importantly, we found straw return significantly altered the community of bacteria involved in the carbon and nitrogen cycle, and their abundance of strong responses depending on the amounts of straw return. For example, straw input increased the abundance of Proteobacteria (+2.64–5.57 %), Acidobacteria (+3.82–13.83 %), and Bacteroidetes (+15.37–30.49 %). Similarly, the amount of straw application increased the bacterial diversity indexes (Shannon, 2.65–10.93 %; Chao1, 13.47–18.50 %), and had significant positive correlations with SOC, TN, and TP contents. Structural equation models (SEM) revealed that straw return management practice had positive and indirect effects on crop yields by influencing soil properties or the bacteria community. In conclusion, our findings revealed common associations and variations of bacterial community diversity with soil factors and crop yields at different straw return rates, and these findings provide insights and options for the development of better straw return strategies and sustainable agriculture in semi-arid regions.

Microplastics stimulated soil bacterial alpha diversity and nitrogen cycle: A global hierarchical meta-analysis

Microplastics (MPs) pollution is recognized as a global emerging threat with serious potential impacts on ecosystems. Our meta-analysis was conducted based on 117 carefully selected publications, from which 2160 datasets were extracted. These publications described experiments in which MPs were added to soil (in laboratory or greenhouse experiments or in the field) after which the soil microbial community was analyzed and compared to a control group. From these publications, we extracted 1315 observations on soil bacterial alpha diversity and richness indices and 845 datasets on gene abundance of bacterial genes related to the soil nitrogen cycle. These data were analyzed using a multiple hierarchical mixed effects meta-analysis. The mean effect of microplastic exposure was a significant decrease of soil bacterial community diversity and richness. We explored these responses for different regulators, namely MPs addition rates, particle size and plastic type, soil texture and land use, and study type. Of the bacterial processes involved in the soil nitrogen cycle, MPs addition significantly promoted assimilation of ammonium, nitrogen fixation and urea decomposition, but significantly inhibited nitrification. These results suggest that MPs contamination may have considerable impacts on soil bacterial community structure and function as well as on the soil nitrogen cycle.

Effects of size and amount and burial depth on early decomposition of maize straw and the links to microbial and nematode communities in the Mollisol of China

AbstractCrop straw is often incorporated into soil at different depths via agricultural practices like tillage, with regional variation in straw decomposition. However, the relative role of management practices on straw decomposition remains unclear. Here, a 5‐month field experiment using litterbags was conducted in three cold sites within China's Mollisol region, with two burial depths (15 and 30 cm) and four maize straw treatments (big straw and small straw at the amounts of 0.5% and 1.0%, respectively). The objectives were to determine the effects of the size and amount and burial depth of straw on its decomposition, microbial and nematode communities, and to identify the key factors regulating straw decomposition. Straw mass loss was affected by straw treatments rather than burial depths in all sites. Specifically, it was the lowest for 0.5% big straw among four straw treatments. Small straw lost more mass than big straw only at the amount of 0.5%, with the variations declining and even disappearing in the site experiencing relatively high temperatures. Microbial biomss and nematode abundance of specific groups were affected by the size and amount of straw in some cases, where the presence of 0.5% big straw corresponded with the lowest microbial biomass and the highest nematode abundance. All bacterial and fungal biomass and some nematode abundances were higher at 30 cm than at 15 cm in the sites with relatively low temperature. The abundance and Shannon index of nematodes were correlated with Gram‐positive bacterial biomass and microbial diversity and evenness index positively, and with other microbial biomass negatively. The straw decomposition explained 83.60% and 77.25% of variations in microbial and nematode community composition, respectively. These results suggest that the physical traits rather than burial depth dominate straw decomposition via changing microbial growth and their interaction with specific nematodes under similar climatic conditions, and the effects of straw physical traits are changed by climate on a large regional scale. Reducing the size and amount is a potential strategy stimulating straw decomposition, particularly in the cold regions.

Designing cropping systems for nickel agromining on ultramafic land in Albania

AbstractAgromining describes the technique of growing plants to “mine” metals present in naturally enriched or contaminated soils. This technique comprises a series of processes including improvement of soil quality and production of biomass in order to obtain metals from the ash of harvested hyperaccumulators, which can be considered bio‐ore. The aim of this study was to evaluate different agronomic practices for Ni agromining of the hyperaccumulator species Odontarrhena chalcidica by analyzing (i) Ni yields and (ii) parameters related to soil fertility, biodiversity, and Ni availability. We tested various types of fertilizers including farmyard manure and assessed cultivation of the hyperaccumulator in either continuous monoculture or cropping in rotation with the legume Vicia ervilia. A 2‐year field experiment was established on typical ultramafic Vertisols in eastern Albania. The current study presents the results obtained in the second year of cultivation. After 2 years of agromining, fertilization with animal manure or rotation with the legume improved several soil properties and increased the yield of phytoextracted Ni by four and five times, respectively, relative to non‐fertilized plots. The fertilization treatments did not affect the bacterial diversity indexes but significantly impacted the bacterial community structure. We suggest a fertilization regime including the application of pig or chicken manure (at doses equivalent to NPK 260:105:260; 260:390:260, respectively) every 2 years or the implementation of crop rotation with legumes as effective strategies for developing Ni agromining on Vertisols.

PSIX-10 Effects of Bacillus subtilis ATCC PTA-122264 on macronutrient digestibility and fecal characteristics, metabolites, and microbiota of healthy adult dogs subjected to an abrupt diet change

Abstract Probiotic use in dogs is increasing, with spore-forming Bacillus species gaining interest due to their viability during processing, storage, and in the gastrointestinal tract. B. subtilis is known for its adaptable metabolism that may be useful in pets subjected to abrupt dietary changes. The objective of this study was to determine dietary apparent total tract macronutrient digestibility (ATTD) and fecal characteristics, metabolites, and microbiota of healthy adult dogs supplemented with B. subtilis ATCC PTA-122264. All procedures were approved by the University of Illinois IACUC prior to experimentation. Dogs [n = 12; 6 ± 1 yr; 8.71 ± 0.91 kg body weight (BW)] were used in a replicated 3x3 Latin square design (n = 12/group) and fed to maintain BW. In each 42-d experimental period, dogs were allotted to one of three treatments: Control (kibble diet only), Low [kibble diet + 1×109 colony-forming units (CFU) of B. subtilis], and High (kibble diet + 5×109 CFU of B. subtilis). After a 22-d adaptation phase, a 5-d fecal collection phase was followed by a blood collection phase. On d 28, dogs were abruptly changed to a canned diet and fed for 14 d, with fecal samples collected on d 30 (2 d post change), 34 (6 d post change), 38 (10 d post change), and 42 (14 d post change). Fecal microbiota data were evaluated using QIIME2. All other data were analyzed using the Mixed Models procedure of SAS, with P &amp;lt; 0.05 being considered significant. B. subtilis supplementation of the kibble diet did not influence food or energy intake, fecal output, ATTD, most serum metabolites, hematology, fecal characteristics, fecal bacterial alpha and beta diversity indices, and dysbiosis index, demonstrating the safety of the strain in dogs. However, fecal Streptococcus and Blautia abundances were higher in High dogs than Low or Control dogs, while E. coli abundance was less in Low dogs than High and Control dogs. The abrupt change to a canned diet led to significant alterations in fecal characteristics, dysbiosis index, and bacterial abundances, which were not influenced by B. subtilis supplementation. Bacterial alpha diversity measures were affected, with observed ASV (amplicon sequence variants) and the Fisher Index reducing, and the Shannon Index increasing by dietary change. The abrupt dietary change caused a distinct shift in microbial communities, as evidenced by principal coordinates analysis plots. The relative abundances of various fecal bacterial taxa, including Bifidobacterium, Faecalibaculum, Turicibacter, and Lactobacillus were decreased, while Collinsella, Ruminococcus gnavus group, and Escherichia-Shigella were increased with the dietary change. Our data support the notion that daily supplementation of 1 – 5×109 CFU of B. subtilis ATCC PTA-122264 in healthy dogs is safe and does not affect markers of general health and fecal characteristics, warranting further exploration.

PSXII-18 Nitrogen balance and ruminal bacterial diversity indexes of Nellore cattle fed with amylolytic and fibrolytic enzymes in feedlot

Abstract This study was carried out to evaluate the use of dietary exogenous enzyme (ENZ) products with amylolytic and fibrolytic activity on nitrogen balance and ruminal alpha and beta diversity of Nellore cattle in feedlot. Rumen cannulated Nellore steers [n = 10; body weigh (BW) = 543 kg ± 28.6 kg] were distributed in a replicate 5 × 5 Latin-square design using individual pens. The treatments consisted of a negative control (CON; without ENZ); Amylase [AML, Amaize, Alltech; 0.5 g/kg of diet dry matter (DM); Xylanase (FBL, Fibrozyme, Alltech; 0.9 g/kg of diet DM]; Half dose (HD; AML 0.25 g/kg of diet DM and FBL 0.45 g/kg of diet DM); and Full dose (FD; AML 0.5 g/kg of diet DM and FBL 0.90 g/kg of diet DM; Table 1). The experimental period lasted 19 d (14 d of adaptation and 5 d of collection). Between d 15 and 18, total urine collection was performed to calculate the nitrogen balance. On d 19 a mixed ruminal sample (6 mL of solid and liquid content) was taken 4 h after feeding and stored at -80 ºC until DNA extraction. Total genomic DNA was extracted using the ZymoBIOMICS DNA Miniprep Kit. The library was prepared using primers for the region V3V4 of the16S rRNA gene; 341F (5’-CCTAYGGGRBGCASCAG-3’) x 806R (5’- GGACTACNNGGGTATCTAAT-3’). The amplicons (~ 470 bp) were sequenced with the Illumina NovaSeq 6000 PE 250 platform. The sequences were analyzed using qiime2 with the SILVA database for the taxonomic assignment. Alpha and beta diversities were calculated in Rstudio using phyloseq. All data were analyzed as orthogonal contrasts assuming treatment as a fixed effect: 1) CON vs. ENZ, 2) AML vs. FBL, 3) HD vs. FD, and 4) AML + FBL vs. HD + FD. Animals that received ENZ had reduced fecal nitrogen excretion (FNE, P = 0.014) and greater efficiency of nitrogen utilization (ENU, P = 0.031) than animals in the CON group. The FBL treatment resulted in greater CP/DOM ratio (P = 0.049), nitrogen balance (P = 0.089), and ENU (P = 0.015) compared with AML treatment. No differences were observed between HD and FD for any nitrogen balance variable (P &amp;gt; 0.10). Animals supplemented with both enzymes (HD + FD) had greater values of N intake (P = 0.018), greater CP/DOM ratio (P = 0.006), and greater FNE (P = 0.002) than animals fed either enzyme alone (AML + FBL). The ENZ supplementation did not impact alpha diversity index or beta diversity (P &amp;gt; 0.10). In conclusion, the addition of exogenous enzymes affected nitrogen balance but not ruminal alpha and beta diversity of Nellore cattle in feedlot.

Characteristic Analysis of the Soil Bacterial Community Structure of Dendrocalamus brandisii from Seven Geographical Provenances in Yunnan Province

Soil is the basis of bamboo growth and quality formation of bamboo shoots and has an important contribution to the sustainable development of agriculture. To this end, We studied the soil properties and microbial communities of Dendrocalamus brandisii by collecting twenty-one soil samples from its seven typical geographic provenances in Yunnan Province, China. Bacterial 16S rRNA gene amplicons were used to detect soil bacteria and predict bacterial functions using Tax4Fun. The results indicated that the soil bacterial diversity indices (ACE, Chao1, Simpson, and Shannon) were significantly different among different geographical provenances. The dominant bacterial groups at the phylum level in all seven regions were Proteobacteria (19.78~29.06%), Actinobacteria (13.53~30.01%), Chloroflexi (8.03~31.47%), and Acidobacteria (7.12~19.17%), with markedly different constitution proportions. Total phosphorus, available potassium, and pH were the main environmental factors affecting soil bacterial communities. There were significant differences in the secondary metabolic pathways and phenotypes of soil bacterial functions, exhibiting a diversity of functions. The geographical variables of the soil bacterial community in D. brandisii varied with spatial scales. Environmental factors such as available potassium (AK), pH, and total nitrogen (TN) have an impact on soil bacterial communities.

The stratified response of heterotrophic, autotrophic or mixotrophic denitrification to enrofloxacin stress along different filling heights in up-flow fixed-bed bioreactors

Antibiotics frequently exist in nitrate wastewater and seriously threaten biological denitrification. This study investigated the impact of enrofloxacin (ENR) on autotrophic, heterotrophic, and mixotrophic denitrification processes at various filling heights. The experiments were conducted across four consecutive phases with ENR concentrations of 0, 0.1, 1, and 10 mg/L. As the influent ENR concentration increased, the denitrification performance of the FeS2-based autotrophic denitrification (PAD) system was significantly inhibited at different filling heights, with nitrate removal efficiency (NrE) dropping to 30.42 %. In contrast, the polycaprolactone (PCL)-based heterotrophic denitrification (PHD) and mixotrophic denitrification (PAD+PHD) systems only affected NrE in the lower layer, whereas the middle and upper layers maintained high NrE levels, largely unaffected by ENR stress, reaching up to 98.28 % and 94.02 % respectively. Sulfate reduction was more prominent in the upper and middle layers of the mixotrophic denitrification bioreactor (PHD system). Bacterial diversity indices initially increased and then decreased as ENR concentration rose from 0 to 10 mg/L, with the PHD system showing lower diversity compared to the PAD system. Redundancy analysis (RDA) revealed that the relative abundances of Proteobacteria and Actinobacteriota in the PAD system, and Bacteroidota and Firmicutes in the PHD system, were negatively correlated with ENR concentration. Overall, the PAD system experienced significant stress from ENR at various filling heights, whereas the upper-middle layer of the PHD system demonstrated greater resistance. This highlighted the impact of antibiotic contamination along with the performance of different filling heights and emphasized the need for tailored strategies in wastewater treatment.

Nonbiodegradable microplastic types determine the diversity and structure of soil microbial communities: A meta-analysis

As an emerging contaminant, microplastics (MPs) have received considerable attention for their potential threat to the soil environment. However, the response of soil bacterial and fungal communities to MPs exposure remains unclear. In this study, we conducted a global meta-analysis of 95 publications and 2317 observations to assess the effects of nonbiodegradable MP properties and exposure conditions on soil microbial biomass, alpha and beta diversity, and community structure. Our results indicate that MPs increased (p < 0.05) soil active microbial biomass by 42%, with the effect varying with MPs type, exposure concentration, exposure time and soil pH. MPs concentration was identified as the most important factor controlling the response of soil microbial biomass to MPs. MPs addition decreased (p < 0.05) the soil bacterial Shannon and Chao1 indices by 2% and 3%, respectively, but had limited effects (p > 0.05) on soil fungal Shannon and Chao1 indices. The type of MPs and exposure time determined the effects of MPs on bacterial Shannon and Chao1 indices, while the type of MPs and soil pH controlled the response ratios of fungal Shannon and Chao1 indices to MPs. Specifically, soil organic carbon (SOC) was the major factor regulating the response ratio of bacterial alpha diversity index to MPs. The presence of MPs did not affect soil bacterial community structure and beta diversity. Our results highlight that MPs reduced bacterial diversity and richness but increased the soil active microbial biomass, suggesting that MPs could disrupt biogeochemical cycles by promoting the growth of specific microorganisms.

Microbiomic and metabolomic dynamics in chrysanthemum waste at different fermentation stages

The microbial community and metabolite profile during the fermentation of chrysanthemum waste (CW) were studied, as well as the effect of feeding fermented chrysanthemum waste (FCW) to sows. The nutritional value of CW fermented for 30–90 days was similar to that of CW fermented for 7 days. With increasing time, the number of bacterial species, richness index, and diversity index increased. The main genera were Pediococcus. A total of 270 different metabolites were identified in FCW, among which benzenoids, amino acids, flavonoids, fatty acids, and peptides were the most significantly different metabolites. Flavone and flavonol biosynthesis, and flavonoid biosynthesis were the most important metabolic pathways in fermentation. Feeding FCW to sows was beneficial for their production performance. These provide new insights into the characteristics of microbiome and metabolome associated with CW during long-term fermentation and the feed availability of FCW.

Differences in Soil Fertility and Bacterial Community Structure Between Carbon Inputs such as Biochar and Organic Fertilizer and Their Relationship

The potato planting area of Guizhou Province ranks second in China. However, due to factors such as climatic conditions and unbalanced fertilization, soil organic matter in potato fields is consumed rapidly and has a large deficit, which affects soil biological function and soil fertility. Biochar and organic fertilizer are effective ways to supplement foreign aid organic matter to improve soil quality. However, the differences in soil fertility and microbial community structure and their relationships under the conditions of organic fertilizer or biochar combined with chemical fertilizer are not clear. In this study, three treatments of conventional fertilization （NPK）, increased application of biochar （NPKB）, and increased application of organic fertilizer （NPKO） were set up to investigate the characteristics of potato rhizosphere soil, bacterial community composition, and diversity； to analyze the effects of these factors on the soil integrated fertility index； and to explore the direct and indirect effects of IFI on soil fertility and bacterial community structure differences between treatments and their driving factors. The results showed that soil pH, available phosphorus （AP）, available potassium （AK）, total nitrogen （TN）, organic carbon （SOC）, and C/N ratio were significantly higher in the NPKB and NPKO treatments than in the NPK treatment （P<0.05）. Soil IFI was greatest for NPKO, followed by NPKB and least for the NPK treatment. A total of 8 214 ASVs were obtained from all the soil samples, belonging to 26 phyla, 75 classes, 165 orders, 176 families, and 251 genera （excluding unidentified fungi）. Proteobacteria, Actinobacteria, and Chloroflexi were the dominant phyla, accounting for 54.85% of all ASVs. Compared to that in the NPK and NPKB treatments, the NPKO treatment had the highest bacterial diversity and number of significantly different taxa, and soil AN, AP, AK, SOC, TN, and IFI were significant correlates of bacterial diversity index （P<0.05）. Additionally, pH, TN, and SOC were significant influencers of bacterial taxa differences （P<0.05）, with importance ranked as TN （70.59%） &gt; SOC （49.42%） &gt; pH （27.08%）. Structural equations suggested that pH-related soil properties and bacterial community diversity were the direct pathways influencing IFI, and soil pH-related soil characteristics could also indirectly affect IFI by affecting bacterial Shannon diversity. These results indicate that soil fertility and bacterial community structure were significantly different and correlated between the biochar and organic fertilizer addition treatments and that pH and bacterial community diversity were the key factors influencing IFI, with the NPKO treatment in particular having the best effect on improving IFI. Considering the effect of soil fertilization and the functional group of bacteria, NPKO is the recommended combination for the best synergistic effect of soil fertilization, that is, N 150 kg·hm-2+P2O5 135 kg·hm-2+K2O 135 kg·hm-2+organic fertilizer 6.6 t·hm-2.

Effects of Different Microbial Fertilizers on Soil Quality and Maize Yield in Coastal Saline Soil

Microbial fertilizers have the characteristics of high efficiency and environmental protection in improving saline soils, and the application of functional microbial fertilizers is of great significance for the green abatement of saline barriers and the improvement of soil quality in coastal areas. The experiment was based on moderately saline soil in the coastal area of Hebei Province, with corn as the indicator crop, on the basis of conventional chemical fertilizer application. Different microbial fertilizer treatments, namely, T1 （conventional chemical fertilizer 750 kg·hm-2 + compound microbial agent 75 kg·hm-2）, T2 （conventional chemical fertilizer 750 kg·hm-2 + Bacillus megaterium 300 kg·hm-2）, T3 （conventional chemical fertilizer 750 kg·hm-2 + B. mucilaginosus 300 kg·hm-2）, T4 （conventional chemical fertilizer 750 kg·hm-2 + organic silicon fertilizer 600 kg·hm-2）, T5 （conventional chemical fertilizer 750 kg·hm-2 + bio-organic fertilizer 600 kg·hm-2）, T6 （conventional fertilizer 750 kg·hm-2 + active microalgae 15 kg·hm-2）, and CK （only fertilizer 750 kg·hm-2）, were used for these seven treatments, to study the effects of different microbial fertilizers on soil nutrients, salinity, bacterial community, and corn yield and economic efficiency during two critical periods （V12 stage and maturity stage） of corn. The results showed that compared with that in CK, T1 significantly increased soil total nitrogen （TN） and available phosphorus （AP） contents during the whole growth period. Over the whole reproductive period, soil organic matter （OM） at maturity increased by 10.35% over the V12 stage compared to that in CK, but there was no significant difference between treatments. Compared with that in CK, T5 and T6 significantly reduced soil total salinity and Ca2+ content during the whole growth period by an average of 14.51%-18.48% and 24.25%-25.51%. T1 significantly increased the bacterial diversity index over the whole growth period by 45.16% compared to that in CK. The dominant soil phyla were Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, and the dominant genera were Bacillus and Geminicoccaceae. The most abundant functions of the bacterial community in the study area were chemoheterotrophy and aerobic chemoheterotrophy, with average relative abundances of 28.89% and 27.11%, and T3 and T6 significantly improved soil N cycling function. The results of redundancy analysis （RDA） indicated that Na+, SO42-, pH, and EC were important factors driving the structure of the bacterial community, and correlation heatmaps showed that Na+, SO42-, pH, and EC were significantly and positively correlated mainly with the phylum Planctomycetota, whereas soil OM and TN were significantly and positively correlated with Cyanobacteria. Compared with that in CK, T6 increased the relative abundance of Cyanobacteria and optimized the bacterial community structure during the whole growth period. Using recommended dosages of bacterial fertilizers T1 and T6 increased maize yield by 7.31%-24.83% and economic efficiency by 9.05%-23.23%, respectively. The preliminary results of soil chemical properties and yield correlation analysis revealed that EC, AP, HCO3-, and Mg2+ were the obstacle factors limiting soil productivity in coastal areas. In conclusion, the use of the compound bacterial agent （T1） and active microalgae （T6） at the recommended dosage can significantly enhance soil nutrients, reduce salinity, and improve the structural diversity of soil bacterial communities, which not only ensures the increase in maize yield and efficiency but also realizes the efficient use of microbial fertilizers and the improvement of soil quality.

Impact of biocrust on soil nitrogen maintenance and microbial composition in citrus orchards under varying urea application rates

Biocrust communities and their effects on soil nitrogen (N) content in natural drylands have been extensively studied. However, their significance in citrus orchards, which are typically managed with N fertilizer, remains unclear. To address this, an investigation was conducted in a citrus orchard subjected to varying levels of urea application (0 %, 70 %, and 100 % of the local N fertilizer application) over three years. The study focused on biocrust communities dominated by bryophytes, examining their community and individual characteristics, and comparing the properties and microbial communities of soils with and without biocrust cover. The results showed that biocrust had the highest percent coverage (56.1 %) in the plot with 70 % local N fertilizer application. Dicranella heteromalla was the dominant biocrust species across all treatments, exhibiting greener and longer leaves with 70 % local N fertilizer application. Biocrust cover significantly (P < 0.01) influenced soil total nitrogen content, soil water content, soil total carbon content, and soil dissolved organic carbon content. In contrast, fertilizer application had non-significant effects on the physicochemical properties of soils, regardless of biocrust cover. A notable difference in bacterial phyla composition was observed between soils with and without biocrust cover (PERMANOVA, P = 0.001), although fertilization did not significantly affect the bacterial diversity index. Additionally, biocrust cover significantly (P < 0.01) influenced predicted soil bacterial functional groups, including ureolysis and nitrogen fixation, while fertilizer application had a weaker impact on these bacterial functional groups. In conclusion, nitrogen application altered the community and dominant species characteristics of biocrust but did not overshadow the effects of biocrust on soil N dynamics. In the citrus orchard with varying levels of urea application, biocrust played a crucial role in soil water retention, N maintenance, and predicted microbial ecological functions related to N cycling.

Effects of Organic Fertilizer Addition to Vegetation and Soil Bacterial Communities in Saline-Alkali-Degraded Grassland with Photovoltaic Panels.

The Songnen grassland is an important resource for livestock production in China. Due to the intensification of anthropogenic activities in recent years, vegetation degradation has worsened, and the salinization of grassland has become increasingly serious, which severely affects the sustainable development of grassland animal husbandry. In this study, organic fertilizer addition was carried out at saline-and-alkaline-degraded Songnen grassland sites with photovoltaic panels, and we investigated the effects of organic fertilizer treatments on the vegetation and soil bacteria in these areas. The results showed that both organic fertilizer treatments increased the community composition and diversity indices of plants (p < 0.05); they also had significant effects on soil electrical conductivity and rapidly available potassium (p < 0.05). In the dominant phylum of bacteria, the relative abundance of Firmicutes increased without adding organic fertilizer under the photovoltaic panel; the addition of organic fertilizer had a significant effect on the relative abundance of Firmicutes and Desulfobacterota (p < 0.05), reducing their relative abundance, respectively. There were differences in the number of bacteria at the genus level under different treatments compared to the control, with the highest enrichment of bacteria occurring at the OFE position, and a significant difference (p < 0.05) being found between the control and the other four groups at the genus level of g_norank_f_norank_o_Actinomarinales. Organic fertilizer had a significant effect on the bacterial Simpson diversity index, with the most significant increasing trend found in OFE (the front eaves of the photovoltaic panel in fertilization area). The results of a correlation analysis showed that pH, electrical conductivity, and total nitrogen were the main factors affecting the soil bacterial community.