Bacterial Biodiversity Research Articles

Influence of Bio-Fertilizer Type and Amount Jointly on Microbial Community Composition, Crop Production and Soil Health

To ensure long-term food production in a changing world, it is critical to identify field management practices that increase crop yields and maintain soil health. Additionally, sustainable agriculture needs to provide experimental evidence to support the use of traditional agricultural practices. In this study, a 20-year investigation of the effects of different combinations of fertilizer types (control, chemical fertilizer, organic fertilizer, and bio-fertilizer) and fertilization amount (conventional dosages and high dosages) on wheat yield and soil health, including soil enzyme activity and microbial biomass, soil microbial diversity, and crop yield. Our long-term study indicates that the use of high dosages of bio-fertilizer can increase the fertilizer yield contribution rate by a minimum of 76.7% compared to other management combinations. Furthermore, this practice can improve soil biological quality, including the concentration of soil microbial biomass carbon, promote bacterial biodiversity, and enhance the soil health index. The effect of high dosages fertilizer was greater than that of conventional dosages fertilizer. The highest soil health index was 0.88 in high dosage bio-fertilizer, and the lowest was 0.12 in chemical fertilizer. In summary, these results suggested that the use of bio-fertilizer can help maintain soil health and crop productivity in the long term.

Biochar + AD exerts a biostimulant effect in the yield of horticultural crops and improves bacterial biodiversity and species richness in the rhizosphere

Organic fertilisers are gaining prominence in advanced agri-systems due to the need for alternatives to the most pollutant agricultural inputs, contributing to sustainable agriculture. The objective of this study was to analyse the agronomic effect of a biochar non-additivated and additivated with anaerobic digestate (AD) on the soil microbiome in melon and pepper crops at the field scale, hypothesising that the synergy between biochar and the additive confers additional benefits to the crop. Two doses of biochar (250 and 500 kg ha−1) and two doses of additive with respect to biochar (5 and 10% v:w) were tested. The highest yield was observed for a reduced dose of mineral fertilisation (NPK −20%) with biochar + AD at the highest dose of additive: a biochar dose of 250 kg/ha with 10% AD for the melon crop and a biochar dose of 500 kg ha−1 with 10% AD for the pepper crop. Specifically, the yield increase compared with the control, which only received NPK, was a 33% increase in melon and 18% in pepper. The microbiome of the bulk soil was not modified by biochar + AD, but the composition of the rhizosphere microbiome changed, emerging plant growth-promoting rhizobacteria (PGPR) or increasing its relative abundance (e.g. Arthrobacter, Mitsuaria or Bacillus genus). We have demonstrated a positive correlation between yield and fruit quality parameters, and the presence of cluster of bacteria with predominance of known PGPR genera, that have been boosted by the treatments with biochar + AD. Thus, we hypothesize that the improved yield and fruit quality is in part due to the rhizosphere bacteria community enhancement.

A DNA-barcode biodiversity standard analysis method (DNA-BSAM) reveals a large variance in the effect of a range of biological, chemical and physical soil management interventions at different sites, but location is one of the most important aspects determining the nature of agricultural soil microbiology

There are significant gaps in our understanding of how to sustainably manage agricultural soils to preserve soil biodiversity. Here we evaluate and quantify the effects of agricultural management and location on soil microbiology using nine field trials that have consistently applied different soil management practices in the United Kingdom using DNA barcode sequence data. We tested the basic hypothesis that various agricultural management interventions have a significant and greater effect on soil bacterial and fungal diversity than geographic location. The analyses of soil microbial DNA sequence data to date has lacked standardisation which prevents meaningful comparisons across sites and studies. Therefore, to analyse these data and crucially compare and quantify the size of any effects on soil bacterial and fungal biodiversity between sites, we developed and employed a post-sequencing DNA-barcode biodiversity standard analysis method (DNA-BSAM). The DNA-BSAM comprises a series of standardised bioinformatic steps for processing sequences but more importantly defines a standardised set of ecological indices and statistical tests. Use of the DNA-BSAM reveals the hypothesis was not strongly supported, and this was primarily because: 1) there was a large variance in the effects of various management interventions at different sites, and 2) location had an equivalent or greater effect size than most management interventions for most metrics. Some dispersed sites imposed the same organic amendments interventions but showed different responses, and this combined with observations of strong differences in soil microbiomes by location tentatively suggests that any effect of management may be contingent on location. This means it could be unreliable to more widely extrapolate the findings from trials performed only at one location. The widespread use of a standard approach will allow meaningful cross-comparisons between soil microbiome studies and thus a substantial evidence-base of the effects of land-use on soil microbiology to accumulate and inform soil management decisions.

Bacterial community diversity and underlying assembly patterns along vertical soil profiles in wetland and meadow habitats on the Zoige Plateau, China

Microorganisms are found throughout the soil, however, our understanding of microbial diversity and the underlying assembling patterns is mostly limited to the surface horizons (0–20 cm). In this study, soil samples were collected from a total of 12 integral vertical soil profiles (from the surface layer to the parent material, up to 5 m depth) from two typical alpine habitats (wetland and meadow) in the Zoige Plateau, China. As determined from 16S rRNA sequencing, soil bacterial diversity and community composition were unique to each habitat. Similar decays in bacterial similarity over distance along soil vertical profiles were observed in both habitats, and taxonomic turnover rates were higher than phylogenetic ones. Bacterial distribution greatly depended on soil depth, with most oligotrophic taxa residing in deeper soil layers. Soil macro-nutrients were major factors regulating bacterial assembly, however, in deeper soil layers with lower nutrient effectiveness, minerals such as manganese, potassium, and sulfur were more influential. Along the whole profile, community assembly was driven mainly by deterministic processes (mostly heterogeneous selection) and to a lesser extent by stochastic processes, as shown by both a null model-based β-nearest taxon index and a normalized stochastic ratio. The habitats differed in the importance of these processes, however, with deterministic processes playing a larger role in bacterial assembly in meadows than in wetlands, and with community members in alpine meadows having narrower environmental thresholds and stronger phylogenetic signals. Additionally, bacterial communities in the subsoil exhibited a narrower niche breadth and were susceptible to deterministic processes. This trend was accompanied by the weaker phylogenetic conservation, suggesting their lower adaptation to environmental changes compared to the topsoil. Overall, our study investigated bacterial biodiversity patterns and the potential processes underlying bacterial assemblage along the vertical soil profile, and provided the first data regarding the vertical geography of soil bacterial communities in typical alpine habitats.

Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.

Culturing the gut microbiota in in vitro models that mimic the intestinal environment is increasingly becoming a promising alternative approach to study microbial dynamics and the effect of perturbations on the gut community. Since the mucus-associated microbial populations in the human intestine differ in composition and functions from their luminal counterpart, we attempted to reproduce in vitro the microbial consortia adhering to mucus using an already established three-dimensional model of the human gut microbiota. Electrospun gelatin structures supplemented or not with mucins were inoculated with fecal samples and compared for their ability to support microbial adhesion and growth over time, as well as to shape the composition of the colonizing communities. Both scaffolds allowed the establishment of long-term stable biofilms with comparable total bacterial loads and biodiversity. However, mucin-coated structures harbored microbial consortia especially enriched in Akkermansia, Lactobacillus, and Faecalibacterium, being therefore able to select for microorganisms commonly considered mucosa-associated in vivo. IMPORTANCE These findings highlight the importance of mucins in shaping intestinal microbial communities, even those in artificial gut microbiota systems. We propose our in vitro model based on mucin-coated electrospun gelatin structures as a valid device for studies evaluating the effects of exogenous factors (nutrients, probiotics, infectious agents, and drugs) on mucus-adhering microbial communities.

Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes

Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

Seasonal and spatial variations of antibiotic resistance genes and bacterial biodiversity in biofilms covering the equipment at successive stages of drinking water purification

The presence of ARGs (antibiotic resistance genes) in the aquatic environment is a serious threat to public health especially in environmental biofilms as natural reservoirs of ARGs in water treatment plants (WTP). It has been shown that the treatment technology and source of water have a significant impact on the abundance and type of genes determining antibiotic resistance. The following indicator genes were proposed that should absolutely be controlled in environmental biofilms: intl1, sul2, sul1, tetA, blaOXA, and blaTEM. In both studied WTPs, the highest number of copies was determined for the intI1 gene. Among the tested ARGs, the highest values were obtained for genes sul1 and tetA. The qPCR analysis also revealed that the amounts of determined ARGs decreased in the following order: sulphonamides>carbapenems >tetracyclines > β-lactams >macrolides. The dominant bacterial types in all analysed samples were Proteobacteria and Bacteroidetes. Both ARGs and bacterial biodiversity was determined rather by sampling site (spatial variation) than seasonality. The obtained results show that biofilms are reservoirs of ARGs. This may affect the microbiological quality of water entering the water system. It is therefore necessary to include their analysis in the classical studies of water quality.

Bacterial diversity in the western slopes of Mount Lawu, Karanganyar, Indonesia

Abstract. Rosariastuti R, Sutami, Nugraha S, Amanto BS. 2023. Bacterial diversity in the western slopes of Mount Lawu, Karanganyar, Indonesia. Biodiversitas 24: 2125-2133. Bacteria are an essential ecosystem component that is critical in nutrient recycling. Mount Lawu is an ecosystem with various habitats supporting bacterial growth. This region contains a diverse range of bacteria that has received little attention. This study aimed to investigate the bacterial biodiversity on Mount Lawu's western slopes of Karanganyar District, Central Java Province, Indonesia based on land use differences. There are five land uses including vegetable plantations, paddy fields, residential, mixed land, and forests. This study is exploratory-descriptive; the survey method and exploration technique are employed. Then, the Next Generation Sequencing (NGS) approach was administered to identify the type of bacteria. This research revealed more than 10 phylum and 28 species of bacteria. The diversity index (H') value was 8.80 for Vegetable plantations, 8.50 for paddy fields, 8.26 for mixed land, 8.10 for residential, and 7.66 for forests, with the highest bacterial diversity index in vegetable plantations. The bacterial diversity incorporates the phylum Proteobacteria, Methylomirabillota, Firmicutes, Actinobacteria, Verrucomicrobiota, Acidobacteriota, Bacteroidota, Myxococcota, Chloroflexi, and others. Phylum Proteobacteria was dominant in each land use, followed by Phylum Actinobacteria. The bacterial diversity on Mount Lawu's western slope was high. This study's findings are useful as a database (information) on microbial biodiversity in Central Java.

Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria Spanning from the South China Sea across the Gulf of Bengal to the Northern Arabian Sea.

Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 μg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.

Exploring Bacterial and Fungal Biodiversity in Eight Mediterranean Olive Orchards (Olea europaea L.) in Tunisia.

A wide array of bacteria and fungi are known for their association with pests that impact the health of the olive tree. The latter presents the most economically important cultivation in Tunisia. The microbial diversity associated with olive orchards in Tunisia remains unknown and undetermined. This study investigated microbial diversity to elucidate the microbial interactions that lead to olive disease, and the bio-prospects for potential microbial biocontrol agents associated with insect pests of economic relevance for olive cultivation in the Mediterranean area. Bacterial and fungal isolation was made from soil and olive tree pests. A total of 215 bacterial and fungal strains were randomly isolated from eight different biotopes situated in Sfax (Tunisia), with different management practices. 16S rRNA and ITS gene sequencing were used to identify the microbial community. The majority of the isolated bacteria, Staphylococcus, Bacillus, Alcaligenes, and Providencia, are typical of the olive ecosystem and the most common fungi are Penicillium, Aspergillus, and Cladosporium. The different olive orchards depicted distinct communities, and exhibited dissimilar amounts of bacteria and fungi with distinct ecological functions that could be considered as promising resources in biological control.

Eukaryotes contribute more than bacteria to the recovery of freshwater ecosystem functions under different drought durations.

Global climate change mostly impacts river ecosystems by affecting microbial biodiversity and ecological functions. Considering the high functional redundancy of microorganisms, the unknown relationship between biodiversity and ecosystem functions obstructs river ecological research, especially under the influence of increasing weather extremes, such as in intermittent rivers and ephemeral streams (IRES). Herein, dry-wet alternation experiments were conducted in artificial stream channels for 25 and 90 days of drought, both followed by 20 days of rewetting. The dynamic recovery of microbial biodiversity and ecosystem functions (represented by ecosystem metabolism and denitrification rate) were determined to analyse biodiversity-ecosystem-function (BEF) relationships after different drought durations. There was a significant difference between bacterial and eukaryotic biodiversity recovery after drought. Eukaryotic biodiversity was more sensitive to drought duration than bacterial, and the eukaryotic network was more stable under dry-wet alternations. Based on the establishment of partial least squares path models, we found that eukaryotic biodiversity has a stronger effect on ecosystem functions than bacteria after long-term drought. Indeed, this work represents a significant step forward for further research on the ecosystem functions of IRES, especially emphasizing the importance of eukaryotic biodiversity in the BEF relationship.

A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation.

Lytic polysaccharide monooxygenases (LPMO) are expected to change the current status of chitin resource utilization. This study reports that targeted enrichment of the microbiota was performed with chitin by the selective gradient culture technique, and a novel LPMO (M2822) was identified from the enrichment microbiota metagenome. First, soil samples were screened based on soil bacterial species and chitinase biodiversity. Then gradient enrichment culture with different chitin concentrations was carried out. The efficiency of chitin powder degradation was increased by 10.67 times through enrichment, and chitin degradation species Chitiniphilus and Chitinolyticbacter were enriched significantly. A novel LPMO (M2822) was found in the metagenome of the enriched microbiota. Phylogenetic analysis showed that M2822 had a unique phylogenetic position in auxiliary activity (AA) 10 family. The analysis of enzymatic hydrolysate showed that M2822 had chitin activity. When M2822 synergized with commercial chitinase to degrade chitin, the yield of N-acetyl glycosamine was 83.6% higher than chitinase alone. The optimum temperature and pH for M2822 activity were 35°C and 6.0. The synergistic action of M2822 and chitin-degrading enzymes secreted by Chitiniphilus sp. LZ32 could efficiently hydrolyze shrimp shell powder. After 12 h of enzymatic hydrolysis, chitin oligosaccharides (COS) yield reached 4,724 μg/mL. To our knowledge, this work is the first study to mine chitin activity LPMO in the metagenome of enriched microbiota. The obtained M2822 showed application prospects in the efficient production of COS.

Antibiotics affected the bacterial community structure and diversity in pore water and sediments with cultivated Phragmites australis in a typical Chinese shallow lake.

The migration of antibiotics and bacterial communities between sediments and pore water occurring in the lake, which is affected by aquatic vegetation. However, the differences in bacterial community structure and biodiversity between pore water and sediments with plants in lakes under antibiotic stress are still poorly understood. We collected pore water and sediments in both wild and cultivated Phragmites australis regions in the Zaozhadian (ZZD) Lake to explore the characteristics of the bacterial community. Our results showed that the diversity of bacterial community in sediment samples were significantly higher than those in pore water samples in both P. australis regions. Due to higher antibiotic levels in sediments from the cultivated P. australis region, the composition of bacterial communities showed a difference, which reduced the relative abundance of dominant phyla in pore water and increased that in sediments. The higher bacterial variations in pore water could be explained by sediment in the cultivated P. australis region than that in wild P. australis region, therefore plant cultivation might change the source-sink pattern between sediments and pore water. The dominant factors shaping the bacterial communities in the wild P. australis region pore water or sediment were NH4-N, NO3-N, and particle size, while cultivated P. australis region pore water or sediment were oxytetracycline, tetracycline, etc. The findings of this work indicates that the antibiotic pollution caused by planting activities has a greater impact on the bacterial community, which will provide a reference for the use and management of antibiotics in lake ecosystems.

Soil oxytetracycline alters the effects of phosphate fertilisation and Bacillus amyloliquefaciens on the bacterial community of Medicago sativa rhizosphere

Introducing specific plant growth-promoting bacteria (PGPB) into the soil ecological system is vital to improve nutrient utilization efficiency. Suitable combinations of inoculant and fertilisation particularly phosphorus (P) play important roles in enhancing the effects of PGPB. The ecotoxic risks of antibiotics in agro-ecosystems are of great concern. A pot experiment was conducted to explore the effects of P fertilisation, Bacillus amyloliquefaciens inoculation, and oxytetracycline (OTC) on the bacterial community and the genes related to soil nitrogen (N) and phosphorus (P) conversion in the rhizosphere of alfalfa. Soil bacterial biodiversity including the number of species and richness was reduced by P fertilisation and OTC addition, enhanced by the inoculation of B. amyloliquefaciens without OTC addition. OTC increased the correlations among bacterial genera. The abundance of total 16S rRNA genes, N- and P-cycling functional genes was decreased by OTC in most cases, but increased at 0 mg P kg−1 and 160 mg OTC kg−1 (P–OTC+) when the soil was inoculated with B. amyloliquefaciens. The relative abundance of five bacterial genera, including Mesorhizobium and some unitalicise uncultured genera, increased at P–OTC+ when inoculated with B. amyloliquefaciens. These genera might use the necromass of some microbes killed by OTC as a nutrient substrate for enhanced growth, thus enhancing the expression of N- and P-cycling functional genes. Overall, OTC altered the effects of P fertilisation and B. amyloliquefaciens inoculation on the bacterial community, N- and P-cycling functional genes in the rhizosphere of alfalfa.

Characteristics of bacterial community structure and diversity in overlying water and sediments with Lotus in the Baiyangdian Lake, China

Bacterial communities in water and sediments are important decomposers of lake ecosystem. However, the differences in bacterial community structure and biodiversity in overlying water and sediments covered by aquatic plants such as Lotus in lake ecosystems are still poorly understood. Here we collected paired overlying water and sediments in the Baiyangdian (BYD) Lake to explore their characteristics of bacterial community. Our results showed that bacterial diversity indices such as Sobs, Shannon, Simpsoneven and Phylogenetic diversity in sediment samples were significantly higher than those in overlying water samples, which were mainly affected by ofloxacin (OFL), dissolved oxygen and pH in the overlying water, while norfloxacin (NOR), OFL and sulfapyridine (SPD) in sediments. Dominant phyla across all overlying water samples were Actinobacteriota (36.65%), Proteobacteria (29.12%) and Patescibacteria (17.01%), while Proteobacteria (20.97%), Chloroflexi (19.56%) and Actinobacteriota (13.37%) in all sediment samples. Source Tracker results showed that about 6.59 ± 1.9% of the variations in bacterial community in sediments could be attributed to the contribution of the overlying water bacterial community, which is higher than that of sediments to the overlying water bacterial community. The dominant factors shaping the bacterial communities in the overlying water were NOR, dissolved organic carbon (DOC) and total phosphorus, while in sediments were NOR, OFL and DOC. It is suggested that antibiotics (especially NOR) may have a substantial effect on bacterial community rather than interaction of environmental compartments (overlying water and sediments), and would help to improve the understanding of bacteria transfer and coalescence in a shallow lake ecosystem.

Winter mulching practice alters soil bacterial communities and networks in lei bamboo (Phyllostachys praecox) forests

AbstractWinter mulching is widely used to raise soil temperature and promote earlier harvesting in agroforestry, but successive years of mulching can lead to soil degradation. The effect of winter mulch on soil bacterial community composition and co‐occurrence patterns is not clear. The influence of different mulches (a defatted seed cake of Camellia oleifera, DS; a mixture of wheat straw and chicken manure, MWC; and wheat straw, WS) on soil bacterial communities and networks in lei bamboo (Phyllostachys praecox) forests over a four‐month mulching period was studied using Illumina sequencing of the 16S rRNA gene. The results showed that mulching time and mulching material treatment significantly influenced bacterial community composition and diversity, mainly driven by nutrient availability. MWC and WS mulching treatments decreased α‐diversity of the bacterial communities, whereas the DS treatment had no significant impact. The oligotrophs, Gryllotalpicola, Granulicella, and Verrucomicrobia, were enriched before and at the end of mulching, while the copiotrophs, Deltaproteobacteria, were enriched in the middle of the mulching period (Jan). Comparing the three mulching treatments, Proteobacteria were enriched in DS mulching soils in Jan. The complexity of the four networks decreased with pre‐mulching, DS mulching, WS mulching, and MWC mulching networks, with a reduction in the number of edges and average degree observed. The results suggested that winter mulching practices adversely affected soil bacterial community diversity and interactions, which may be detrimental to the resistance of bacterial communities to environmental changes and soil sustainability. Mulching MWC and WS has a greater risk of loss of soil bacterial biodiversity than DS.

Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study.

The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.

Bacterial communities of Antarctic lichens explored by gDNA and cDNA 16S rRNA gene amplicon sequencing.

Recently, lichens came once more into the scientific spotlight due to their unique relations with prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper, we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the nonactive part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.

Carbon Amendments Shape the Bacterial Community Structure in Salinized Farmland Soil.

Practical, effective, and economically feasible salt reclamation and amelioration methods are in great demand in arid and semiarid areas. Energy amendments may be more appropriate than alternatives for improving salinized farmland soil because of their effects on soil microbes. We investigated the effects of biochar (Carbon) addition and desulfurization (noncarbon) on the soil bacterial community associated with Zea mays seedlings. Proteobacteria, Firmicutes, and Actinobacteriota were the dominant soil bacterial phyla. Biochar significantly increased soil bacterial biodiversity but desulfurization did not. The application of both amendments stimulated a soil bacterial community shift, and biochar amendments relieved selection pressure and increased the stochasticity of community assembly of bacterial communities. We concluded that biochar amendment can improve plant salt resistance by increasing the abundance of bacteria associated with photosynthetic processes and alter bacterial species involved in carbon cycle functions to reduce the toxicity of soil salinity to plants. IMPORTANCE Farmland application of soil amendments is a usual method to mitigate soil salinization. Most studies have concluded that soil properties can be improved by soil amendment, which indirectly affects the soil microbial community structures. In this study, we applied carbon and noncarbon soil amendments and analyzed the differences between them on the soil microbial community. We found that carbon soil amendment distinctly altered the soil microbial community. This finding provides key theoretical and technical support for using soil amendments in the future.

Plant functional trait diversity and structural diversity co-underpin ecosystem multifunctionality in subtropical forests

Tree species diversity is assumed to be an important component in managing forest ecosystems because of effects on multiple functions or ecosystem multifunctionality. However, the importance of tree diversity in determining multifunctionality in structurally complex subtropical forests relative to other regulators (e.g., soil microbial diversity, stand structure, and environmental conditions) remains uncertain. In this study, effects of aboveground (species richness and functional and structural diversity) and belowground (bacterial and fungal diversity) biodiversity, functional composition (community-weighted means of species traits), stand structure (diameter at breast height and stand density), and soil factors (pH and bulk density) on multifunctionality (including biomass production, carbon stock, and nutrient cycling) were examined along a tree diversity gradient in subtropical forests. The community-weighted mean of tree maximum height was the best predictor of ecosystem multifunctionality. Functional diversity explained a higher proportion of the variation in multifunctionality than that of species richness and fungal diversity. Stand structure -played an important role in modulating the effects of tree diversity on multifunctionality. The work highlights that species composition and maximizing forest structural complexity are effective strategies to increase forest multifunctionality while also conserving biodiversity in the management of multifunctional forests under global environmental changes.