Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas

The abundance and pathogenicity of microbes in automobile air conditioning filters across the typical cities of China and Europe

Bioaerosols are widely distributed in urban air and can be transmitted across the atmosphere, biosphere, and anthroposphere, resulting in infectious diseases. Automobile air conditioning (AAC) filters can trap airborne microbes. In this study, AAC filters were used to investigate the abundance and pathogenicity of airborne microorganisms in typical Chinese and European cities. Culturable bacteria and fungi concentrations were determined using microbial culturing. High-throughput sequencing was employed to analyze microbial community structures. The levels of culturable bioaerosols in Chinese and European cities exhibited disparities (Analysis of Variance, P < 0.01). The most dominant pathogenic bacteria and fungi were similar in Chinese (Mycobacterium: 18.2-18.9 %; Cladosporium: 23.0-30.2 %) and European cities (Mycobacterium: 15.4-37.7 %; Cladosporium: 18.1-29.3 %). Bartonella, Bordetella, Alternaria, and Aspergillus were also widely identified. BugBase analysis showed that microbiomes in China exhibited higher abundances of mobile genetic elements (MGEs) and biofilm formation capacity than those in Europe, indicating higher health risks. Through co-occurrence network analysis, heavy metals such as zinc were found to correlate with microorganism abundance; most bacteria were inversely associated, while fungi exhibited greater tolerance, indicating that heavy metals affect the growth and reproduction of bioaerosol microorganisms. This study elucidates the influence of social and environmental factors on shaping microbial community structures, offering practical insights for preventing and controlling regional bioaerosol pollution.

Initial soil condition, stand age, and aridity alter the pathways for modifying the soil carbon under afforestation

Afforestation is a crucial pathway for ecological restoration and has the potential to modify soil microbial community, thereby impacting the cycling and accumulation of carbon in soil across diverse patterns. However, the overall patterns of how afforestation impacts below-ground carbon cycling processes remain uncertain. In this comprehensive meta-analysis, we systematically evaluated 7045 observations from 210 studies worldwide to evaluate the influence of afforestation on microbial communities, enzyme activities, microbial functions, and associated physicochemical properties of soils. Afforestation increases microbial biomass, carbon and nitrogen hydrolase activities, and microbial respiration, but not carbon oxidase activity and nitrogen decomposition rate. Conversely, afforestation leads to a reduction in the metabolic quotient, with significant alteration of bacterial and fungal community structures and positive effects on the fungi: bacteria ratio rather than alpha and beta diversity metrics. We found a total 77 % increase in soil organic carbon (SOC) content after afforestation, which varied depending on initial SOC content before afforestation, afforestation stand age, and aridity index of afforestation sites. The modified SOC is associated with bacterial community composition along with intracellular metabolic quotient and extracellular carbon degrading enzyme activity playing a role. These findings provide insights into the pathways through which afforestation affects carbon cycling via microorganisms, thus improving our knowledge of soil carbon reservoir's responses to afforestation under global climate change.

Soil microbial community structure, function and network along a mangrove forest restoration chronosequence

Mangrove forests have high ecological, social and economic values, but due to environmental changes and human activities, natural mangrove forests have experienced serious degradations and reductions in distribution area worldwide. In the coastal zones of southern China, an introduced mangrove species, Sonneratia apetala, has been extensively used for mangrove restoration because of its rapid growth and strong environmental adaptability. However, little is known about how soil microorganisms vary with the restoration stages of the afforested mangrove forests. Here, we examined the changes in soil physicochemical properties and microbial biomass, community structure and function, and network in three afforested S. apetala forests with restoration time of 7, 12, and 18 years and compared them with a bare flat and a 60-year-old natural Kandelia obovata forest in a mangrove nature reserve. Our results showed that the contents of soil salinity, organic carbon, total nitrogen, ammonium nitrogen, and microbial biomass increased, while soil pH and bacterial alpha diversity decreased with afforestation age. Soil microbial community structure was significantly affected by soil salinity, organic carbon, pH, total nitrogen, ammonium nitrogen, available phosphorus, and available kalium, and susceptibility to environmental factors was more pronounced in bacterial than fungal community structure. The relative abundances of aerobic chemoheterotrophy were significantly higher in 12- and 18-year-old S. apetala than in K. obovata forest, while that of sulfate-reducing bacteria showed a decreasing trend with afforestation age. The abundance of dung saprotroph was significantly higher in 12- and 18-year-old S. apetala forests than in the natural forest. With the increasing afforestation age, the modularity of microbial networks increased, while stability and robustness decreased. Our results suggest that planting S. apetala contributes to improving soil fertility and microbial biomass but may make soil microbial networks more vulnerable.

Effects of hexabromocyclododecane and polyethylene microplastics on soil bacterial communities

Hexabromocyclododecane (HBCD) and polyethylene (PE) microplastic are ubiquitous pollutants, and knowledge about the effects of HBCD and PE pollution on soil bacterial communities remains obscure. In this study, the effects of different HBCD and PE concentrations and combined HBCD and PE exposure on the diversity, composition, and function of agricultural soil bacterial communities over 4 months were systematically examined for the first time. Generally, soil bacterial communities were influenced in both the 1-month and 4-month scenarios through HBCD and PE separately as well as combined exposure. After 4 months of exposure, PE and combined exposure significantly affected soil bacterial alpha diversity, however, low concentration of HBCD showed no apparent influence. 1-month and 4-month HBCD, PE, and combined exposure significantly influenced bacterial beta diversity. Compared with 1 month of exposure, HBCD, PE, and combined exposure demonstrated remarkable influences on soil bacteria after 4 months of exposure, especially on Nitrospirae, Elusimicrobia, Rokubacteria at the phylum level, and on MND1, Ruminiclostridium, Lysobacter, Anaeromyxobacter, Alistipes, WCHB1 at the genus level. The bacterial function analysis indicated that amino acid metabolism, carbohydrate metabolism, and membrane transport were the three predominant enriched bacterial functions after 1-month and 4-month HBCD and PE exposure. This research provides a comprehensive grasp of the effects of HBCD and PE pollution on soil microbial communities, which could have a beneficial impact on future soil pollution control.

Assessment of the Fruit Chemical Characteristics and Antioxidant Activity of Different Mulberry Cultivars (Morus spp.) in Semi-Arid, Sandy Regions of China

As a traditional cash crop with ecological and nutritional values, mulberry is gradually expanding its consumption worldwide due to its great regional adaptability and superior health functions. The widespread interest in nutrients has led to a growing need to explore in depth the health benefits of mulberries. Many studies are actively being conducted to investigate the adaptability of the diversity of mulberries in different applications. This study systematically investigated the physicochemical properties and antioxidant activity of four mulberry genotypes cultivated in China's semi-arid sandy regions to better understand the composition and health-promoting potential of this super crop. Chemical composition identification was identified via HPLC and antioxidant activity was further determined via DPPH and FRAP. The moisture, crude protein, ash, soluble solids, phenolics, anthocyanins, and flavonoids contents of mulberry were comparatively analyzed. The study revealed that the four mulberry genotypes showed significant differences in quality and content of the analyzed characteristics. The greatest antioxidant activity was found in Shensang 1, which had the most soluble solids (17%) and the highest amounts of free sugar (fructose: 5.14% and glucose: 5.46%). Ji'an had the most minerals (K: 2.35 mg/g, Ca: 2.27 mg/g, and Fe: 467.32 mg/kg) and it also contained chlorogenic acid, which has the potential to be turned into a natural hypoglycemic agent. PCA and Pearson correlation analysis indicated that the antioxidant activity was closely related to the chemical contents of total phenols, flavonoids, anthocyanins, and soluble sugars. If the antioxidant activity and nutrient content of the developed plants are considered, Shen Sang 1 is the most favorable variety. This finding can be used to support the widespread cultivation of mulberries to prevent desertification as well as to promote the development of the mulberry industry.

Composition and diversity of soil bacterial communities under identical vegetation along an elevational gradient in Changbai Mountains, China

Soil bacteria play important roles in biogeochemical cycling and biodiversity in mountain ecosystems. Past studies have investigated the bacterial community composition and diversity in elevation gradations covered by different vegetation types, but for a better assessment of elevation effects, here we studied bacterial communities in soil under identical vegetation cover. High-throughput amplicon sequencing of the V3-V4 region of bacterial 16S rDNA was used to investigate the diversity and composition bacterial communities in soil from 700 to 1,000 m above sea level collected on the north slope of Changbai Mountains, Northeast China. Obviously differences (p &lt; 0.05) in soil physicochemical parameters (i.e., total nitrogen, nitrate and ammonium nitrogen, soil moisture content, available potassium, microbial biomass carbon and nitrogen) were observed at different elevations. Soil bacterial abundance indices (Richness, Chao1, ACE) differed significantly along the elevation gradient, whereas the Shannon index remained unchanged. Principal Coordinates Analysis indicated separated soil bacterial communities of the different elevations. The dominant phyla in all soil samples were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Bacteroidetes, which in combination reached 80%–85%. Soil pH to some extend related to soil bacterial community along altitude gradations. The relative abundance of a multiple phyla was negatively affected by the soil nutrients, such as ammonium and nitrate nitrogen, available potassium, soil moisture content, available phosphorus, microbial biomass nitrogen and soil organic C. The strongest effects were seen for Proteobacteria. The pH either positively or negatively correlated with specific genera. The soil bacterial function differed significantly among four elevations. The chemoheterotrophy, aerobic chemoheterotrophy and nitrification were the most dominant functions of soil bacteria among four elevations. Overall, the changes in soil physicochemical properties with elevation are important in shaping the bacterial diversity, composition and function in soil with the same above-ground vegetation of Changbai Mountains.

Impact of environmental factors and bacterial interactions on dust mite allergens in different indoor dust

Indoor dust is the main carrier of indoor pollutants, especially dust mite allergens and bacteria, they can trigger asthma, rhinitis, eczema and other allergic diseases. However, the interactions between dust mite allergens and bacterial communities in different types of indoor dust are not clear. The study focused on particulate and flocculent fibrous dust, explored the concentrations of Der p 1 (Dermatophagoides pteronyssinus) and Der f 1 (D. farinae) in 46 households in Changchun and their environmental influences, characterized the bacterial communities by high-throughput sequencing, and the interactions between Der p 1, Der f 1 and bacterial communities were explored. The results showed that Der p 1 and Der f 1 tended to accumulate more in flocculent fibrous dust, and Der p 1 predominated in the indoor dust samples. The floor height, years of housing occupancy and the living areas all affected the concentrations of dust mite allergens. In bacterial community, Proteobacteria, Firmicutes and Actinobacteria were leading phyla in the two types of dust. Kocuria, Blastococcus and Massilia were dominating genera in particulate dust and Acinetobacter, Lactobacillus, Corynebacterium_1 were dominating genera in flocculent fibrous dust. The overall diversity and species richness of bacteria in particulate dust were significantly higher than those in flocculent dust (p < 0.001). The living area was an important environmental factor affecting the bacterial community in flocculent fibrous dust (p < 0.01). The interaction between the relative abundance of Proteobacteria, Firmicutes and Actinobacteria and dust mite allergen concentrations significantly differed between the two dust types, indicating that bacteria could be used both as food and to establish symbiotic relationships with household dust mites (HDMs) hosts and provide nutrition.

Response of bacterial community structure to different ecological niches and their functions in Korean pine forests

A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.

Comparative effects of environmental factors on bacterial communities in two types of indoor dust: Potential risks to university students

University students are constantly exposed to potential bacterial pathogens and environmental pollutants in indoor environment because they spend most of their time indoors. University dormitory and printing shop are two typical indoor environments frequented by university students. However, little is known about the characteristics of bacterial community as well as the effect of indoor environmental factors on them. 16S rRNA gene sequencing was used to reveal the bacterial community in indoor dust, electronic devices were recorded during dust sampling, and polybrominated diphenyl ethers (PBDEs) were detected by gas chromatography mass spectrometry (GC-MS). Proteobacteria, Actinobacteria and Firmicutes were leading phyla, and Acinetobacter, Paracoccus and Kocuria were dominating genera. The predominant genera showed Acinetobacter > Paracoccus > unidentified Corynebacteriaceae in indoor dusts from university dormitories, whereas Paracoccus > unidentified Cyanobacteria > Acinetobacter in printing shops. The occurrence of Acinetobacter, Kocuria, Corynebacterium, Pseudomonas, and Bacillus suggested the health risks of potential pathogenic bacteria to university students. Significant differences of microbial composition and diversity were proved between university dormitories and printing shops. Chemoheterotrophy and aerobic chemoheterotrophy were dominant bacterial functions, and the seven primary bacterial functions displayed university dormitory > printing shop. BDE 138 and BDE 66 were main environmental parameters affecting the indoor dust bacterial community in university dormitory, while printer and BDE 47 played dominating role in shaping microorganism in printing shop. The complex biotic (potential bacterial pathogens) and abiotic factors (electronic equipment and chemical pollutants) in indoor dusts may pose potential health risks to university students.

Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil

Atrazine is one of the most widely used herbicides, however it and its metabolites cause widespread contamination in soil and ground water. Bioaugmentation is an effective method for remediation of environmental organic pollutants. High-throughput sequencing provides an important tool for understanding the changes of microbial community and function in response to pollutants degradation based on bioaugmentation. In this study, the effect of biodegradation with Paenarthrobacter sp. W11 and the change of microbial community during atrazine degradation were investigated. The results showed that bioaugmentation significantly accelerated the degradation rate of atrazine in soil and reduced the toxic effect of atrazine residues on wheat growth. The extra available NH₄⁺ through atrazine mineralization could serve as a nitrogen source to increase microbial numbers. High-throughput sequencing further revealed that the microbial community restored a new balance. The function of microbial community predicted by PICRUSt2 suggested that the biodegradation process of atrazine affected not only the atrazine degradation pathway, but also the nitrogen metabolism pathway. Methylobacillus and Pseudomonas were considered as the most important indigenous atrazine-degrading microorganisms, because their relative abundances were positively correlated with the relative abundance of Paenarthrobacter and atrazine degradation pathway. This study provides insight into the cooperation between indigenous microorganisms and external inoculums on atrazine degradation process.

Untangling the response of fungal community structure, composition and function in soil aggregate fractions to food waste compost addition

Soil fungi are key drivers in regulating the ecosystem function, playing a vital role in protecting the plant from phytopathogens and other biotic and abiotic pressures. However, the potential impact of compost addition and soil aggregate size on the fungal community and functional ecological guild remains uncertain. This study investigated the structure, composition, and function of soil fungal communities across aggregate fractions under food waste compost addition using Miseq sequencing and FUNGuild. Compost addition exerted a negative impact on fungal α-diversity, and shifted the structure and changed the composition of fungal community. Compost addition rates exhibited more contributions to fungal α-diversity variations (R = 0.609, 0.895, and 0.501 for Sobs, Shannon, and Chao indices, respectively, P = 0.001) and the separation of community structure than soil aggregate size (R = 0.952, P = 0.001). Biomarkers, including Chaetomiaceae, Ascobolaceae, and Sordariomycete, displayed significant superiority in compost-added soils, whereas the populations of Nectriaceae and Clavicipitaceae were significantly decreased. The relative abundances of animal and plant pathogens were significantly decreased, whereas that of saprotrophs were increased. The abundances of pathogens correlated positively with pH and negatively with nutrients (soil organic matter, dissolved organic carbon, total nitrigen, NH₄⁺, and NO₃^-), whereas those of saprotrophs showed an opposite trend. The dose of compost was the major driver for fungal functional guild variation, whereas carbon and nitrogen source exhibited more contributions to function variation than pH value. These results provide a reference for sustainable ecological agriculture by applying compost rationally under the conditions of soil health and agricultural performance.

Can We Use Functional Annotation of Prokaryotic Taxa (FAPROTAX) to Assign the Ecological Functions of Soil Bacteria?

FAPROTAX is a promising tool for predicting ecological relevant functions of bacterial and archaeal taxa derived from 16S rRNA amplicon sequencing. The database was initially developed to predict the function of marine species using standard microbiological references. This study, however, has attempted to access the application of FAPROTAX in soil environments. We hypothesized that FAPROTAX was compatible with terrestrial ecosystems. The potential use of FAPROTAX to assign ecological functions of soil bacteria was investigated using meta-analysis and our newly designed experiments. Soil samples from two major terrestrial ecosystems, including agricultural land and forest, were collected. Bacterial taxonomy was analyzed using Illumina sequencing of the 16S rRNA gene and ecological functions of the soil bacteria were assigned by FAPROTAX. The presence of all functionally assigned OTUs (Operation Taxonomic Units) in soil were manually checked using peer-reviewed articles as well as standard microbiology books. Overall, we showed that sample source was not a predominant factor that limited the application of FAPROTAX, but poor taxonomic identification was. The proportion of assigned taxa between aquatic and non-aquatic ecosystems was not significantly different (p > 0.05). There were strong and significant correlations (σ = 0.90–0.95, p < 0.01) between the number of OTUs assigned to genus or order level and the number of functionally assigned OTUs. After manual verification, we found that more than 97% of the FAPROTAX assigned OTUs have previously been detected and potentially performed functions in agricultural and forest soils. We further provided information regarding taxa capable of N-fixation, P and K solubilization, which are three main important elements in soil systems and can be integrated with FAPROTAX to increase the proportion of functionally assigned OTUs. Consequently, we concluded that FAPROTAX can be used for a fast-functional screening or grouping of 16S derived bacterial data from terrestrial ecosystems and its performance could be enhanced through improving the taxonomic and functional reference databases.

Long-term effects of two organic amendments on bacterial communities of calcareous mediterranean soils degraded by mining

The application of organic amendments to improve the chemical and biological properties of degraded soils from calcareous quarries is necessary to accelerate restoration processes. The aim of this study is to assess the success of different restoration treatments in the long-term using two organic amendments (sewage sludge from urban waste water (SS) and compost from domestic solid waste (CW)). The chemical properties and bacterial communities of restored soils were compared with unamended soils (NA) and surrounding natural soils (NS) from a limestone quarry in a semi-arid ecosystem. After 10 years of the addition of organic amendments, the abundance of soil bacteria, diversity, and taxonomic composition at the phylum and genus level in each soil type was analysed by rRNA 16 S amplification (PCR), sequencing using Illumina, and comparison with the SILVA database using QIIME2 software. The relationships between soil bacterial taxa and chemical soil properties (pH, electrical conductivity (EC), total organic carbon (TOC), and total nitrogen content (TN)) were also studied, as well as the interrelations between soil bacterial taxa at the genus level or the next upper taxonomic level identified. The organic amendments changed the chemical properties of the restored soils, influencing the microbial communities of the restored soils. CW treatment was the organic amendment that most resembled NS, favouring in the long-term a greater diversity and proliferation of bacteria. Several bacterial communities, more abundant in NA and CW soils, were strongly correlated with each other (Craurococcus, Phaselicystis, Crossiella, etc.), forming a bacterial co-occurrence pattern (Co-occurrence pattern 1). Those bacteria showed high significant positive correlations with TOC, TN, and EC and negative correlations with the soil pH. In contrast, NA soils presented other groups of bacterial communities (Co-occurrence pattern 2) represented by Sphingomonas, Rubellimicrobium, Noviherbaspirillum, Psychroglaciecola and Caenimonas, which showed high significant positive correlations with soil pH and negative correlations with TOC, TN, and EC. The distance-based redundancy analysis indicated that SS soils remained in an intermediate stage of chemical and biological quality between NS and NA soils. Our results demonstrate that soil chemical properties and soil bacterial communities significantly changed with organic amendments in calcareous Mediterranean soils degraded by mining.