Soil properties influence bacterial abundance and diversity under different land-use regimes in semi-arid environments

A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain®) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community

The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.

Organic amendments modulate the crop yield and rhizospheric bacterial community diversity: a 3-year field study with Cajanus cajan

Excessive use of chemicals to enhance soil nutrient status and crop yield has resulted in a decline in soil health. Organic farming promotes organic amendments, which help to balance the ecosystem. Understanding the dynamic patterns of belowground microbial populations is essential for developing sustainable agricultural systems. Therefore, the study was designed to evaluate the effect of different agri-practices on rhizospheric bacterial diversity and crop yield in an Indian agricultural system. A 3-year field experiment was set up in a randomized block design using Cajanus cajan as a model crop, comparing conventional farming with organic practice (with animal manure and bio-compost as amendments). Plant and rhizospheric soil samples were collected at the harvest stage for assessing various growth attributes, and for characterizing rhizospheric bacterial diversity. Enhanced crop productivity was seen in conventional farming, with a 2.2-fold increase in grain yield over control. However, over the 3 years, an overall positive impact was observed in the bio-compost-based organic amendment, in terms of bacterial abundance, over other treatments. At the harvest stage of the third cropping season, the bacterial diversity in the organic treatments showed little similarity to the initial bacterial community composition of the amendment applied, indicating stabilization along the growth cycles. The study emphasizes the significance of the choice of the amendment for ushering in agricultural sustainability.

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality

BACKGROUND

Bacterial community found in biodynamic preparations (BD500-BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

RESULTS

Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

CONCLUSION

The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.

Exploring the relationship between metal(loid) contamination rate, physicochemical conditions, and microbial community dynamics in industrially contaminated urban soils

Increasing metal(loid) contamination in urban soils and its impact on soil microbial community have attracted considerable attention. In the present study, the physicochemical parameters and the effects of twelve metal(loid) pollution on soil microbial diversity, their ecotoxic effects, and human health risk assessment in urban soils with different industrial background were studied in comparison with an unpolluted forest soil sample. Results showed that urban soils were highly contaminated, and metal(loid) contamination significantly influenced structure of the soil microbial communities. In all samples the bacterial community was dominated by Proteobacteria, and on the level of phyla characteristic differences were not possible to observe between polluted and control sampling sites. However, clear differences emerged at class and genus level, where several rare taxa disappeared from contaminated urban soils. Simper test results showed that there is 71.6 % bacterial OTU and 9.5 % bacterial diversity dissimilarity between polluted and control samples. Ratio of Patescibacteria, Armatimonadetes, Chlamydiae, Fibrobacteres, and Gemmatimonadetes indicated a significant (p < 0.05) positive correlation with soil Zn, Cr, Pb, Sn, Cu, Mn content, suggest that metal(loid)s strongly influence the structure of microbial community. In contrast, the presence of metal(loid) contamination in urban soils has been found to significantly reduce the population of Archaeal communities. This can be attributed to the depletion of organic matter caused by contamination that reached a minimum of 0.5 m/m% for nitrate and 0.9 m/m% for total organic carbon. The values of urban soil pH were close to neutral, ranging from 5.9 to 8.3. The findings of ecotoxicology test are alarming, as all the studied urban soil sites were cytotoxic to soil microorganisms, and in one site metal(loid) contamination reached genotoxic level. Moreover, all the metal(loid) contaminated sites pose severe and persistent health risk to children, highlighting the urgent need for effective measures to mitigate metal(loid) pollution in urban areas.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Study of polycyclic aromatic hydrocarbons accumulation in bioretention facilities and its influence on microbial community structure

Bioretention facilities are one of the most widely used measures for urban stormwater control and utilization. In this study, the accumulation characteristics of polycyclic aromatic hydrocarbons (PAHs) in bioretention facilities and the effects of PAHs on the structure of microbial communities were explored by combining on-site monitoring and water distribution simulation experiments. The correlation between pollutant accumulation and dominant microorganisms in the bioretention systems was also clarified. The results showed that all 16 priority PAHs were detected in the bioretention facilities in the sponge city pilot area. The PAH concentrations in the soil during the non-rainy season were higher than those in the rainy season and medium- and high-ring PAHs dominated. PAHs in the study area were mainly derived from coal and biomass combustion. The potential carcinogenic risk of PAHs accumulated in the bioretention facilities in the study area was low. The microbial diversity during the non-rainy season was greater than that during the rainy season. Firmicutes, Bacteroidetes, Bacteroides, and Massilia were strongly correlated with naphthalene (NAP), pyrene (PYR), fluoranthene (FLT), and benzo[a]pyrene (BaP). According to the results of the small-scale water distribution test, the addition of PAHs had little effect on the decline in water quantity, and there was no significant regularity in the reduction of water quality including TP, NH4+-N, NO3-N, and TN. The addition of PAHs had a significant effect on the microbial community structure and an inhibitory effect on enzyme activity.

Characterizing indigenous plant growth promoting bacteria and their synergistic effects with organic and chemical fertilizers on wheat (Triticum aestivum)

The excessive use of chemical fertilizers is deteriorating both the environment and soil, making it a big challenge faced by sustainable agriculture. To assist the efforts for the solution of this burning issue, nine different potential native strains of plant growth-promoting bacteria (PGPB) namely, SA-1(Bacillus subtilis), SA-5 (Stenotrophomonas humi),SA-7(Azospirillum brasilense), BH-1(Azospirillum oryzae), BH-7(Azotobacter armeniacus), BH-8(Rhizobium pusense), BA-3(Azospirillum zeae), BA-6(Rhizobium pusense), and BA-7(Pseudomonas fragi) were isolated that were characterized morphologically, biochemically and molecularly on the basis of 16S rRNA sequencing. Furthermore, the capability of indigenous PGPB in wheat (Triticum aestivum, Chakwal-50) under control, DAP+FYM, SA-1,5,7, BH-1,7,8, BA-3,6,7, DAP+ FYM + SA-1,5,7, DAP+FYM+ BH-1,7,8 and DAP+FYM+ BA-3,6,7 treatments was assessed in a randomized complete block design (RCBD). The results of the study showed that there was a significant increase in plant growth, nutrients, quality parameters, crop yield, and soil nutrients at three depths under SA-1,5,7, BH-1,7,8, and BA-3,6,7 in combination with DAP+FYM. Out of all these treatments, DAP+ FYM + BA-3,6,7 was found to be the most efficient for wheat growth having the highest 1000-grain weight of 55.1 g. The highest values for plant height, no. of grains/spike, spike length, shoot length, root length, shoot dry weight, root dry weight, 1000 grain weight, biological yield, and economic yield were found to be 90.7 cm, 87.7 cm, 7.20 cm, 53.5 cm, 33.5 cm, 4.87 g, 1.32 g, 55.1 g, 8209 kg/h, and 4572 kg/h, respectively, in the DAP+FYM+BA treatment. The DAP+FYM+BA treatment had the highest values of TN (1.68 µg/mL), P (0.38%), and K (1.33%). Likewise, the value of mean protein (10.5%), carbohydrate (75%), lipid (2.5%), and available P (4.68 ppm) was also highest in the DAP+FYM+BA combination. C:P was found to be significantly highest (20.7) in BA alone but was significantly lowest (11.9) in DAP+FYM+BA. Hence, the integration of strains BA-3, BA-5, and BA-7 in fertilizers can be regarded as the most suitable choice for agricultural growth in the sub-mountainous lower region of AJK. This could serve as the best choice for sustainable wheat growth and improved soil fertility with lesser impacts on the environment.

Humate application alters microbiota-mineral interactions and assists in pasture dieback recovery

Pasture dieback is a rapidly expanding decaying pasture syndrome that affects millions of hectares of agricultural land in Queensland, Australia, making it useless for the cattle industry and decimating farmers' income and welfare. Since the syndrome was first identified in the early 1990s, farmers and agronomists have tried various methods for pasture recovery, including slashing, burning, ploughing and resowing grass, fertilising, destocking, and overstocking. In most cases, after a minimal initial improvement, the grass reverts to dieback within a few weeks. Here, we present an application of potassium humate, a well-known plant growth stimulator, as a possible long-term recovery option. Humate was applied once at the rate of 12 ml per m². Humate application did not alter the alpha or beta diversity of soil bacterial communities, nor did it change the mineral profile in the soil. However, humate application altered soil microbiota-mineral temporal interactions and introduced subtle changes in the microbial community that could assist pasture recovery. A single humate application increased paddock plant biomass significantly up to 20 weeks post-application. Eleven months after the single application, the paddock was grazed to the ground by the cattle just before the rainfall season. After pasture regrowth, the humate-treated plots significantly improved root morphometric indicators for both grass and dicots and increased the ratio of grass/weeds by 27.6% compared to the water-treated control. While this treatment will not resolve the dieback syndrome, our results invite more research to optimise the use of humate for maximum economic benefit in paddock use under pasture dieback syndrome conditions.

Soil organic carbon, total nitrogen stocks and CO2 emissions in top- and subsoils with contrasting management regimes in semi-arid environments

This study aims to investigate soil organic carbon (SOC) and total nitrogen (TN) contents and stocks, CO₂ emissions and selected soil properties in croplands, grazing lands, exclosures and forest lands of semi-arid Ethiopia. Sampling was done at 0-30, 30-60 and 60-90 cm soil depths and concentration and stocks of SOC, TN and selected soil properties were determined using standard routine laboratory procedures. There were variations in distribution of SOC and TN stock over 90 cm depth across land use types and locations, decreasing from topsoils to subsoil, with average values ranging from 48.68 Mg C ha^-1 and 4.80 Mg N ha^-1 in Hugumburda cropland to 303.53 Mg C ha^-1 and 24.99 Mg N ha^-1 in Desa'a forest respectively. Forest sequestered significant higher SOC and TN stock, decreasing with depth, compared with other land use types. In Desa'a and Hugumburda, the conversion of forest to cropland resulted in a total loss of SOC stock of 9.04 Mg C ha^-1 and 2.05 Mg C ha^-1, respectively, and an increase in CO₂ emission of 33.16 Mg C ha^-1 and 7.52 Mg C ha^-1 yr^-1, respectively. The establishment of 10 years (Geregera) and 6 years (Haikihelet) exclosures on degraded grazing land increased SOC stock by 13% and 37% respectively.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.

Influence of Nutrients and the Native Community on E. coli Survival in the Beach Environment

Previous research has identified E. coli populations that persist in freshwater beach sand distinct from fecal pollution events. This work identifies factors that influence the survival of E. coli in sand using laboratory microcosms to replicate beach conditions. Microcosms were deployed to examine the effect of genetic background, competition with native microbial community, and increased nutrient concentrations on E. coli survival. Survival was comparable between the phylotypes B1 and B2, however, deficiency of stress response greatly reduced survival. In the absence of the native community under nutrient conditions comparable to those observed in sand, E. coli cell densities remained within an order of magnitude of initial concentrations after 5 weeks of incubation. Increased nitrogen was associated with decreased decay rates in the first 2 weeks, and increased carbon appeared to provide an advantage at later time points. However, the highest survival was found with the addition of both carbon and nitrogen. Native sand seeded with fresh Cladophora maintained higher concentrations of E. coli, compared to sand containing decayed Cladophora or no Cladophora. Our findings demonstrate persistent E. coli populations in sand can be affected by the availability of carbon and nitrogen, the ability to regulate stress, and the presence of algal mats (i.e., Cladophora). Further, this work suggests that the native microbial communities may modulate survival by outcompeting E. coli for nutrients. IMPORTANCE Current monitoring for fecal pollution does not account for persistent E. coli populations in freshwater sand, which can result in higher concentrations in water when no threat to human health is present. This work examined the drivers for persistent E. coli populations in sand to aid beach management techniques. We examined the influence of nutrients, including localized sources such as stranded Cladophora, on E. coli populations. We found the major determinant of E. coli survival in freshwater beach sand was the addition of nutrients, specifically carbon and nitrogen concentrations 10-fold higher than baseline concentrations on beaches. This work provides the framework for identifying pollution sources that can promote E. coli survival in sand through the characterization of carbon and nitrogen content, which can be incorporated into beach management techniques. Through this improved knowledge, we can begin to understand E. coli fluctuations in water due to resuspension from sand into water.

The diversity of rhizospheric bacterial communities associated with Trichoderma-treated rice fields

Microbial-based fertilizer has been widely used as a healthier and better alternative to agrochemical products. However, the effects of biofertilizers on the rhizospheric microbiota has rarely been investigated. Thus, the aim of this study was to investigate the effects of symbiotic fungus Trichoderma asperellum SL2-based inoculant on the soil bacterial population through next generation sequencing using a metabarcoding approach. The treatments plots were treated with T. asperellum SL2 spore suspension, while the control plots were treated with sterilized distilled water. The results showed similar bacterial microbiome profiles in the soil of control and T. asperellum SL2-treated plots. In conclusion, the application of the T. asperellum SL2 inoculant had not exerted negative impact towards the bacterial population as similar observation was reflected in control plots. Nonetheless, future research should be conducted to investigate the effects of repeated application of T. asperellum SL2 over a longer period on the rice microbiota communities.

Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze-Thaw Cycles

In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing-thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing-thawing in a glass greenhouse, followed by 64 days under freezing-thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze-thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing-thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing-thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing-thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing-thawing. Moreover, exposure to freezing-thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing-thawing greatly affected soil microbiome composition, biochar reduced the freeze-thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing-thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.

Microbial communities in carbonate precipitates from drip waters in Nerja Cave, Spain

Research on cave microorganisms has mainly focused on the microbial communities thriving on speleothems, rocks and sediments; however, drip water bacteria and calcite precipitation has received less attention. In this study, microbial communities of carbonate precipitates from drip waters in Nerja, a show cave close to the sea in southeastern Spain, were investigated. We observed a pronounced difference in the bacterial composition of the precipitates, depending on the galleries and halls. The most abundant phylum in the precipitates of the halls close to the cave entrance was Proteobacteria, due to the low depth of this sector, the direct influence of a garden on the top soil and the infiltration of waters into the cave, as well as the abundance of members of the order Hyphomicrobiales, dispersing from plant roots, and other Betaproteobacteria and Gammaproteobacteria, common soil inhabitants. The influence of marine aerosols explained the presence of Marinobacter, Idiomarina, Thalassobaculum, Altererythrobacter and other bacteria due to the short distance from the cave to the sea. Nineteen out of forty six genera identified in the cave have been reported to precipitate carbonate and likely have a role in mineral deposition.

Land-Use Driven Changes in Soil Microbial Community Composition and Soil Fertility in the Dry-Hot Valley Region of Southwestern China

The Dry-Hot Valley is a unique geographical region in southwestern China, where steep-slope cultivation and accelerating changes in land-use have resulted in land degradation and have aggravated soil erosion, with profound impacts on soil fertility. Soil microbes play a key role in soil fertility, but the impact of land-use changes on soil microbes in the Dry-Hot Valley is not well known. Here, we compared characteristics and drivers of soil microbial community composition and soil fertility in typical Dry-Hot Valley land uses of sugarcane land (SL), forest land (FL), barren land (BL) converted from former maize land (ML), and ML control. Our results showed that BL and SL had reduced soil organic carbon (SOC), total nitrogen (TN), and total potassium (TK) compared to ML and FL. This indicated that conversion of ML to SL and abandonment of ML had the potential to decrease soil fertility. We also found that fungal phyla Zoopagomycota and Blastocladiomycota were absent in SL and BL, respectively, indicating that land-use change from ML to SL decreased the diversity of the bacterial community. Redundancy analysis indicated that the relative abundance of bacterial phyla was positively correlated with TN, SOC, and available potassium (AK) content, and that fungal phyla were positively correlated with AK. Land-use indirectly affected the relative abundance of bacterial phyla through effects on soil moisture, clay, and AK contents, and that of fungal phyla through effects on clay and AK contents. In addition, land-use effects on bacteria were greater than those on fungi, indicating that bacterial communities were more sensitive to land-use changes. Management regimes that incorporate soil carbon conservation, potassium addition, and judicious irrigation are expected to benefit the stability of the plant–soil system in the Dry-Hot Valley.

Untangling the Rhizosphere Bacterial Community Composition and Response of Soil Physiochemical Properties to Different Nitrogen Applications in Sugarcane Field

Minimizing the use of chemical fertilizers and investigating an appropriate ecofriendly level of nitrogen fertilizer is the key to sustainable agriculture. Sugarcane is the main cash crop of China, especially in the Guangxi region. Information regarding the effect of different nitrogen levels on sugarcane rhizosphere microbiota is still limited. In this study, we evaluated the effect of four different levels of nitrogen fertilizers on rhizosphere bacterial composition using high throughput sequencing, along with soil physiochemical properties, sugarcane agronomic and yield performance. The four treatment combinations were CK (no fertilizers), L (Low, 100 kg ha^–1), M (Medium, 150 kg ha^–1), and H (High, 200 kg ha^–1). The results showed that M nitrogen application significantly altered the rhizosphere bacterial community, soil properties, and sugarcane yield. The richness and evenness of the bacterial community were higher in M treatment than CK. In M treatment important bacterial phyla Acidobacteria and Proteobacteria increased by 47 and 71%, respectively; and at genus level, Acidothermus and Bradyrhizobium increased by 77.2 and 30.3%, respectively, compared to CK. Principal component analysis (PCA) and cluster analysis further confirmed the level of differences among the treatments. The PCA analysis explained 80% of the total variation among the treatments. Spearmen correlation heatmap showed that environmental factors such as pH, AP (available phosphorous), AK (available potassium), and SCAT (soil catalase) were the key factors impacting sugarcane rhizosphere microbiome composition. The H and L nitrogen application alter the bacterial community and sugarcane performance but the M nitrogen application appears to be ecofriendly, productive, and an appropriate nitrogen application rate that could be further used in the Guangxi region.

Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert

Simple Summary

We present a systematic investigation of the distribution of microbial communities in arid and semi-arid regions of Thar Desert Rajasthan, India. Their responses in multiple environmental stresses, including surface soil, surface water and underground water were evaluated. We further assess the biotechnological potential of native microorganisms and discover functional species with results providing a detailed understanding of the abundance of microbial communities in these regions, associated with various stress-related biogeochemical and biotechnological processes. We hope our work will facilitate the development of effective future strategies for the use of extremophiles in complex environments.

Abstract

The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications.

Assessing bacterial diversity and antibiotic resistance dynamics in wastewater effluent-irrigated soil and vegetables in a microcosm setting

Water scarcity is one of the main challenges in sustainable agricultural development particularly in developing countries therefore, irrigation of food crops with wastewater effluent has become a common practice in order to meet the growing food demand. The aim of this study was to determine the impact of wastewater irrigation on bacterial community and antibiotic resistance dynamics in soil and vegetables in an agricultural setting. To determine bacterial diversity, occurrence and overall dynamics of antibiotic resistant genes (ARGs) in effluent irrigated soil and vegetables, 16S rRNA gene metagenomics, shotgun metagenomics and molecular PCR technique were utilized. A shift in bacterial community profile was observed as notable reduction in proteobacteria and increase in firmicutes phyla from the microcosm soil following wastewater effluent irrigation. Shotgun metagenomics revealed diverse ARGs belonging to at least nine different classes of antibiotics in the effluent wastewater. However, only bla_TEM (beta-lactamase) and aadA (aminoglycoside) resistance gene sequences were identified in microcosm soil following irrigation and only bla_TEM was detected on effluent irrigated vegetable surfaces (spinach and beetroots). From the study, only bla_TEM gene was identified across all samples; effluent wastewater, effluent-treated soil, and vegetables. The data suggests a possible dissemination and persistence of the beta-lactamase bla_TEM gene from effluent wastewater into agricultural soil and vegetables. This study enhances our understanding of antibiotic resistance spread and highlights the importance of monitoring antibiotic resistance in agro-systems, which is critical for informing policies aimed at sustainable use of wastewater effluent in water-stressed countries.

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Wastewater effluent potentially introduces antibiotic resistance genes into the soil and vegetables.

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The beta-lactamase (bla_TEM) gene from effluent wastewater is potentially introduced into agricultural soil and vegetables.

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Monitoring antibiotic resistance in agro-systems is critical for informing policies aimed at sustainable use of wastewater.

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Irrigation with wastewater effluent remains unregulated in most developing countries.

Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa

Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO₃) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction

We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.

Smallholder Farmers' Practices and African Indigenous Vegetables Affect Soil Microbial Biodiversity and Enzyme Activities in Lake Naivasha Basin, Kenya

Simple Summary

Smallholder farmers in Sub-Saharan Africa (SSA) are food insecure. Underexploited African indigenous vegetables (AIVs) are consumed locally without being considered a primary source of food and income. However, AIVs hold great potential for the future challenges of food security and climate change. We investigated the effects of different cropping systems and inclusion of AIVs in farming on the soil biodiversity and fertility status of smallholder farmers in Naivasha, Kenya. Compared to mainstream farming approaches, soil microorganisms under AIV cultivations differed significantly. Tillage, fertilization, soil amendments, and traditional homemade plant protection were singled out as the most important factors. The soil alteration index based on enzyme activity offered a reliable way to determine the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future and may contribute to the mitigation of food insecurity.

Abstract

Loss of soil biodiversity and fertility in Sub-Saharan Africa (SSA) may put the food security of smallholder farmers in peril. Food systems in SSA are seeing the rise of African indigenous vegetables (AIVs) that are underexploited but locally consumed without being considered a primary source of food and income. Here we present a field study, a first of its kind, in which we investigated the effects of different cropping systems and inclusion of AIVs in the farming approach on bacterial and fungal biodiversity and community structures, enzymatic activity, and the alteration status of soils of the smallholder farmers in Kenya. When compared to mainstream farming approaches, the composition and biodiversity of bacteria and fungi under AIV cultivations was significantly different. Tillage had a significant impact only on the fungal communities. Fertilization and soil amendments caused shifts in microbial communities towards specialized degraders and revealed the introduction of specific microorganisms from amendments. Traditional homemade plant protection products did not cause any disturbance to either of soil bacteria or fungi. The soil alteration index based on enzyme activity successfully differentiated the alteration status for the first time in SSA. These findings could be useful for farmers to integrate AIVs with correct sustainable practices for a sustainable future.

Bacterial community dynamics in tropical soil after sewage sludge amendment

Although the widespread use of sewage sludge in developing countries is common, little is known about how sludge disposal can affect the microbial composition and diversity of tropical soils. We evaluated the effects of the sewage sludges of two types of anaerobic digestors differing, by the biological treatment they have undergone (uplow anaerobic sludge blanket and activated sludge digester), and two different disposal methods (surface and incorporated) on tropical soils. Samples were taken from topsoil (0-10 cm) and analyzed by amplifying the 16S rRNA genes to study the microbial community, and physicochemical analysis was performed concomitantly. The results indicated that, in general, sewage sludge amendment (SSA) significantly changed the tropical soil bacterial community by the sludge type and by application method. Moreover, the redundancy analysis diagram indicates that changes in soil chemical parameters over time due to SSA resulted in changes in the bacterial community's composition, increasing the population responsible for recycling nutrients in the soil.