Rhizosphere Soil Samples Research Articles

In vitro Evaluation of Biocontrol Potential of Lactic Acid Bacteria Isolated from Natural Ecosystem against Plant Pathogenic Fungi

Lactic acid bacteria (LAB) are ubiquitous, Gram-positive, fermentative bacteria, which are regarded as safe for both humans and the environment. The present study aimed to evaluate the biocontrol efficiency of LAB isolated from different natural ecosystems against fungal pathogens. A total of 30 LAB was isolated from rhizosphere soil and phyllosphere sample of Solanaceous crop viz., Brinjal, Capsicum, Chilli, Tomato, whey, and sauerkraut out of them 14, 9, 4 and 3 lactic acid bacteria (LAB) were isolated from rhizosphere soil & phyllosphere sample of Solanaceous crops, whey and Sauerkraut respectively. The biocontrol ability of LAB isolates were tested against fungal plant pathogens such as Fusarium oxysporum, Pythium aphanidermatum, Sclerotium rolfsi, Rhizoctonia solani, Alternaria sp. agar well diffusion assay and mycelial growth inhibition in liquid culture. The results indicated that the isolates LAB 4, LAB 10, LAB 22, LAB 24 and LAB 29 were prominent in inhibiting the growth of most of the pathogens. Molecular characterization of selected LAB isolates revealed that LAB 4, LAB 10, LAB 22, LAB 24 belongs to Lactobacillus plantarum and LAB 29 belong to Leuconostoc mesentroides.

Isolation and Characterization of Novel Biological Control Agent Clostridium beijerinckii against Meloidogyne incognita.

One of the most severe soil-borne pathogens in the world is the root-knot nematode (Meloidogyne incognita). Biological control is gaining more importance as environmental awareness increases. Thus, keeping this in mind, a total of 712 bacterial strains were isolated from 117 rhizosphere soil samples and investigated for potential biological control activity against M. incognita. Strain Sneb518 (Clostridium beijerinckii) was identified as having solid biocontrol activity against M. incognita. Sneb518 demonstrated significant inhibition against M. incognita, with J2 mortality reaching 90.73% at 12 h and with eggs hatching at a rate of 6.00% at 24 h, compared to a hatchability level of 29.07% for the control. Additionally, Sneb518 was excellent for enhancing seed germination. The seeds coated with a fermentation broth containing Sneb518 efficiently boosted the germination rate to 88.49%. The effectiveness and stability of C. beijerinckii Sneb518 against M. incognita were then further evaluated in a greenhouse. According to the pot experiment data, Sneb518 considerably (p < 0.05) reduced the number of root galls and egg masses on roots and also significantly (p < 0.05) increased tomato plant growth. C. beijerinckii Sneb518-treated tomato seedlings exhibited 50.26% biocontrol effectiveness compared to the control group. Our results demonstrate that C. beijerinckii Sneb518 can be a potential biological control agent against root-knot nematode disease and a biomass enhancer. This research will give new options for the sustainable control of root-knot nematode disease in tomatoes and other host plants.

Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland

The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance–decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.

Composition and Structural Characteristics of Rhizosphere Microorganisms of Polygonum sibiricum (Laxm.) Tzvelev in the Yellow River Delta

The Polygonum sibiricum (Laxm.) Tzvelev, an important herbal species used to protect seawalls, has a solid resistance to salinity and alkali and can grow on alkali spots in saline–alkali soils. So far, the composition, population, and characteristics of its rhizosphere biological community related to the adaptation salt–alkali environment were still unknown. In the present study, rhizosphere and non-rhizosphere soil samples from the P. sibiricum on Chenier Island were collected. High-throughput sequencing was conducted to obtain the structural diversity of rhizosphere microbial communities. Our results showed that the dominant bacteria groups in the rhizosphere and non-rhizosphere were Proteobacteria, Actinobacteriota, Gemmatimonadota, and Actinobacteriota. The dominant fungi groups in the rhizosphere and non-rhizosphere soil samples were Ascomycota, Basidiomycota, Chytridiomycota, and Mortierellomycota. The results of the ASVs (amplicon sequence variants) showed that fungi have more ASVs in common. The PERMANOVA analysis showed that the bacteria among different groups were significantly different. The PCoA (principal coordinates analysis) study also showed that the structures of the bacterial and fungal communities between the rhizosphere and non-rhizosphere were distinct. Function results showed that the relative abundance in COG (Clusters of Orthologous Groups of proteins) functional annotation was significantly different between the two groups. In addition to the general function prediction and carbohydrate transport and metabolism, the COG of the non-rhizosphere was higher than that of the rhizosphere. Our findings benefited the knowledge for studying and conserving the molecule-level adaptive mechanisms of P. sibiricum.

Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines.

Soil microbiota plays a significant role in plant development and health and appears to be a major component of certain forms of grapevine decline. A greenhouse experiment was conducted to study the impact of the microbiological quality of the soil and grapevine rootstock genotype on the root microbial community and development of young plants. Two rootstocks heterografted with the same scion were grown in two vineyard soils differing in microbial composition and activities. After 4 months, culture-dependent approaches and amplicon sequencing of bacterial 16S rRNA gene and fungal ITS were performed on roots, rhizosphere and bulk soil samples. The root mycorrhizal colonization and number of cultivable microorganisms in the rhizosphere compartment of both genotypes were clearly influenced by the soil status. The fungal diversity and richness were dependent on the soil status and the rootstock, whereas bacterial richness was affected by the genotype only. Fungal genera associated with grapevine diseases were more abundant in declining soil and related root samples. The rootstock affected the compartmentalization of microbial communities, underscoring its influence on microorganism selection. Fluorescence in situ hybridization (FISH) confirmed the presence of predominant root-associated bacteria. These results emphasized the importance of rootstock genotype and soil composition in shaping the microbiome of young vines.

Exploration And Identification Of Antagonic Fungi On The Rhizosphere Of Clove Plants (Syzygium aromaticum L.) In Ambon Island

Antagonistic fungi are a group of fungi that can suppress or inhibit the growth and development of plant pathogens. This study aimed to isolate the fungus from the rhizosphere of the clove plant (Syzygium aromaticum L.) from two sub-districts of Leihitu Barat and Leihitu, and to test the ability of these isolates to inhibit Rizoctonia solani. Exploration was carried out using the simple random sampling method, taking rhizosphere soil samples from clove plants from Hatu, Allang, Asilulu and Seith. Then isolated by the dual culture method after that, identified based on the identification key book and calculated its inhibition against plant pathogens. The results showed that 10 fungal isolates were identified, namely 4 fungal genera, namely Trichoderma, Aspergillus, Penicillium and Rhyzopus. The soil around the rhizosphere of clove plants contains antagonistic fungi that can inhibit the growth of tomato sprouting pathogens (Rhizoctonia solani). Obtained 7 isolates of the antagonist fungus Trichoderma sp. with the results of the antagonism test showing the highest inhibition was achieved by isolates of TrichoRCTAL2 (89,52%), and the lowest percentage was by isolates of TrichoRCTAS4 (44,07%).

Root-associated fungal microbiota of the perennial sweet sorghum cultivar under field growth.

Root-associated fungal microbiota, which inhabit the rhizosphere, rhizoplane and endosphere, have a profound impact on plant growth and development. Sorghum bicolor (L.) Moench, also called broomcorn or sweet sorghum, is a multipurpose crop. The comparison between annual and perennial sweet sorghum cultivars in terms of plant growth, as well as their interactions with belowground fungal microbiota, is still poorly understood, although there has been growing interest in the mutualism between annual sweet sorghum and soil bacteria or bacterial endophytes. In this study, the perennial sweet sorghum cultivar N778 (N778 simply) and its control lines TP213 and TP60 were designed to grow under natural field conditions. Bulk soil, rhizosphere soil and sorghum roots were collected at the blooming and maturity stages, and then the fungal microbiota of those samples were characterized by high-throughput sequencing of the fungal ITS1 amplicon. Our results revealed that the alpha diversity of the fungal microbiota in rhizosphere soil and root samples was significantly different between N778 and the two control lines TP213 and TP60 at the blooming or maturity stage. Moreover, beta diversity in rhizosphere soil of N778 was distinct from those of TP213 and TP60, while beta diversity in root samples of N778 was distinct from those of TP213 but not TP60 by PCoA based on Bray-Curtis and WUF distance metrics. Furthermore, linear discriminant analysis (LDA) and multiple group comparisons revealed that OTU4372, a completely unclassified taxon but with symbiotroph mode, was enriched in sorghum roots, especially in N778 aerial roots at the blooming stage. Our results indicate that Cladosporium and Alternaria, two fungal genera in the rhizosphere soil, may also be dominant indicators of sorghum yield and protein content in addition to Fusarium at the maturity stage and imply that the perennial sweet sorghum N778 can primarily recruit dominant psychrotolerant bacterial taxa but not dominant cold-tolerant fungal taxa into its rhizosphere to support its survival below the freezing point.

Zinc-Solubilizing Streptomyces spp. as Bioinoculants for Promoting the Growth of Soybean (Glycine max (L.) Merrill).

Zinc-solubilizing bacteria can convert the insoluble form of zinc into soluble forms available to plants. This study was conducted to isolate and screen zinc-solubilizing actinobacteria from rhizosphere soils and to assess their effect on vegetable soybean growth. In total, 200 actinobacteria strains belonging to 10 genera were isolated from rhizosphere soil samples. Among these isolates, four showed zinc solubilization with solubilizing index values ranging from 3.11 to 3.78 on Bunt and Rovira agar supplemented with 0.1% zinc oxide. For the quantitative assay, in broth culture, strains CME34 and EX51 solubilized maximum available zinc contents of 529.71 and 243.58 μg/ml. Furthermore, indole-3-acetic acid (IAA) and ammonia were produced by these two strains, the strain CME34 produced the highest amount of IAA 4.62 μg/ml and the strain EX51 produced the highest amount of ammonia 361.04 μg/ml. In addition, the phosphate-solubilizing abilities in Pikovskaya's medium of CME34 and EX51 were 64.67 and 115.67 μg/ml. Based on morphological and biochemical characterization and 16S rDNA sequencing, the strains CME34 and EX51 were closely related to the genus Streptomyces. In a greenhouse experiment, single-strain inoculation of Streptomyces sp. CME34 or EX51 significantly increased the shoot length, root length, plant dry weight, number of pods per plant and number of seeds per plant of vegetable soybean plants compared to the uninoculated control. These findings facilitated the conclusion that the two Streptomyces strains have potential as zinc solubilizers and can be suggested as bioinoculants to promote the growth and yield of soybean.

Antagonism of Rhizosphere Streptomyces yangpuensis CM253 against the Pathogenic Fungi Causing Corm Rot in Saffron (Crocus sativus L.).

Plant diseases lead to a significant decline in the output and quality of Chinese herbal medicines. Actinomycetes play a vital role in the rhizosphere ecosystem. This is especially true for Streptomyces, which have become a valuable biological control resource because of their advantages in producing various secondary metabolites with novel structures and remarkable biological activities. The purpose of this study was to isolate an effective antagonistic actinomycete against the pathogen of corm rot in saffron. An antagonistic actinomycete, CM253, was screened from the rhizosphere soil samples of Crocus sativus, by plate co-culture with four pathogenic fungi (Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, and Penicillium citrinum). CM253 inhibited the growth and development of F. oxysporum hyphae by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Furthermore, by analyzing the degrading enzyme, the growth-promoting performance, and the whole genome of strain CM253, it was identified as Streptomyces yangpuensis, which produces NH3, protease, glucanase, cellulase, IAA, and ACC deaminase. In addition, 24 secondary metabolite synthesis gene clusters were predicted in antiSMASH. We identified genes encoding 2,3-butanediol; methionine; isoprene (metH, mmuM, ispEFH, gcpE, idi, and ilvABCDEH); biofilm formation; and colonization (upp, rfbBC, efp, aftA, pssA, pilD, fliA, and dhaM). Above all, S. yangpuensis CM253 showed the potential for future development as a biocontrol agent.

Mixed grass species differ in rhizosphere microbial community structure and function response to drought compared to monocultures

Natural grassland succession is the interactions among different grass species and various environmental factors. The dynamics of soil microbial communities along succession stages has received tremendous attention. The effects of the coexistence of different grass species on the structure and function of rhizosphere soil microbial communities, however, are poorly understood, especially under drought stress conditions. Here, we investigated how different grass planting patterns and soil water content affect rhizosphere microbial community structure and function. Two typical grass species (Bothriochloa ischaemum and Stipa bungeana) on the Loess Plateau were planted in three planting systems: B. ischaemum monoculture, S. bungeana monoculture, and a mixed culture of the two species under two water regimes (optimal water: 80% field capacity [FC]; drought stress: 60% FC). Rhizosphere soil samples were collected to evaluate the rhizosphere microbial community structure (via phospholipid fatty acid [PLFA] biomarkers) and function (via six enzyme activities). The mixed culture of grass species noticeably shifted the rhizosphere microbial community structure. It caused the rhizosphere gram-positive:gram-negative PLFA ratio and fungal:bacterial PLFA ratio to increase under optimum water conditions. In comparison, drought stress caused total PLFA, bacterial PLFA, and gram-positive PLFA biomass to increase. Drought stress caused rhizosphere-specific enzyme activity to increase under monoculture treatment and rhizosphere-specific enzyme activity to decrease under mixed culture treatment. Soil water-soluble organic carbon, pH, and water-soluble organic phosphorus were the most important factors driving changes to rhizosphere microbial community composition. In comparison, pH was the predominant factor driving variation in rhizosphere specific enzyme activities. Thus, the coexistence of grass species altered the structure and function of the rhizosphere microbial community through changes in rhizosphere pH and water-soluble nutrients. In conclusion, changes to rhizodeposits under a mixed culture of grass species likely affect the structure and function of the rhizosphere microbial community. The results of the present study improve our understanding of the impacts of grass species interaction on soil biogeochemical processes under future global drought stress scenarios.

Description of three novel species of Scandinavium: Scandinavium hiltneri sp. nov., Scandinavium manionii sp. nov. and Scandinavium tedordense sp. nov., isolated from the oak rhizosphere and bleeding cankers of broadleaf hosts.

While investigating the bacterial populations of environmental samples taken from a mix of healthy and Acute Oak Decline afflicted Quercus robur (pedunculate or English oak) rhizosphere soil samples and swabs of bleeding lesions on Tilia spp. (lime) and Quercus rubra (red oak) trees, several strains belonging to the order Enterobacterales were isolated using selective media and enrichment broth. Seven strains from the Q. robur rhizosphere, three strains from Tilia spp. and one from Q. rubra were investigated, with their taxonomic status determined via a polyphasic taxonomic approach. Initially stains were identified as potential members of the recently described genus Scandinavium, based on the partial sequencing of three housekeeping genes. Further analysis of phenotypic traits, including fatty acid profiles, coupled with 16S rRNA gene and phylogenomic analysis of whole genome sequences were applied to a subset of the strains. Phylogenetic and phylogenomic analysis repeatedly placed the isolates in a monophyletic clade within Scandinavium, with four distinct clusters observed, one of which corresponded to Scandinavium goeteborgense, the type species of the genus. The remaining three clusters could be phenotypically and genotypically differentiated from each other and S. goeteborgense. As such, we describe three novel species of the genus, for which we propose the names Scandinavium hiltneri sp. nov. (type strain H11S7T = LMG 32612T = CCUG 76179T), Scandinavium manionii sp. nov. (type strain H17S15T = LMG 32613T = CCUG 76183T) and Scandinavium tedordense sp. nov. (type strain TWS1aT = LMG 32614T = CCUG 76188T). Additionally, the descriptions of the genus Scandinavium and the type species, S. goeteborgense, are emended.

Linking rhizospheric microbial and fine root C:N:P stoichiometry under long-term forest conversion

The rhizosphere is the microbial hotspot, while fine roots (diameter <2 mm) are the most physiologically active component in forests. However, how rhizospheric microbial carbon (C): nitrogen (N): phosphorus (P) stoichiometry (ESm) is linked with fine root C:N:P stoichiometry (ESfr) in response to long-term forest conversion remains largely unexplored. Using a space-for-time substitution method, we investigated long-term conversion from natural forests (NF) to plantations of Metasequoia glyptostroboides (MG), Cryptomeria fortunei (CF) and Cunninghamia lanceolata (CL). Fine root and rhizospheric soil samples (0–10 cm depth) were collected, and their C, N and P contents were determined. The rhizospheric soil microbial community (SMC) structure, as well as microbial biomass C, N and P, was measured. Both ESm and ESfr present strict homeostasis and ESm did not significantly correlated with the SMC structure or the microenvironment, suggesting that C and nutrient processes via fine roots and rhizospheric microbes return to equilibrium after long-term forest conversion. Moreover, ESm was synergistically and tightly linked with ESfr, indicating that P deficiency was aggravated during NF-to-CF conversion but ameliorated during NF-to-MG and NF-to-CL conversions. The linkage between ESm and ESfr could act as a robust ecological indication of nutrient-use strategies and limitations in forest ecosystems, benefiting our understanding on C and nutrient cycling regarding forest management.

Seedling growth promotion and potential biocontrol against phytopathogenic Fusarium by native rhizospheric Pseudomonas spp. strains from Amarillo Zamorano maize landrace

Maize is one of the most important staple crops around the word. In Mexico, Los Altos de Jalisco is an agricultural region with the highest production of maize with rainfed irrigation, an agronomic management based on the use of no longer sustainable agrochemicals, and sowing of coated seeds of different commercial origin. Nowadays, the microbiota associated to the rhizosphere of native landraces is considered a reservoir of microbial resources with the potential to promote plant growth and control diseases. With the aim to find ecofriendly and cost-effective alternatives that can reduce the use of agrochemicals at seed germination and seedling growth of maize crop in Los Altos de Jalisco, this study focused on the search of fluorescent Pseudomonas strains as germination and seedlings growth promoters and biocontrol agents of fusariosis in maize, and highlight the importance of Mexican maize landraces as natural reservoirs of plant growth-promoting microorganisms. Samples of rhizospheric soil and seeds were collected from ten maize landraces and a pure line. Pseudomonas and Fusarium strains were isolated and selected by its antagonistic and pathogenic potential, respectively. Pseudomonas strains were phylogenetically identified by a 16S rRNA gene analysis, and Fusarium strains by the phylogenetic analysis of ITS region. The potential of Pseudomonas strains to promote seed germination and seedling/plant growth was explored through metabolic profiles and bioassays to evaluate bacteria-plant-fungus interactions. A total of 57 Fusarium spp. strains were grouped into four different Fusarium species complexes and 14 fluorescent Pseudomonas strains were classified into four Pseudomonas fluorescens subgroups. Pseudomonas strains displayed plant growth promotion and biocontrol capacity by increasing 38%–66% the dry weight of maize seedlings (p < 0.05), 23%–63% growth-inhibition of different Fusarium strains in dual cultures, and a range of 4.5–20 inhibition score based on a rate scale when inoculated in seeds. Pseudomonas spp. metabolic profiles were diverse, but all the strains proved to be innocuous, and Pseudomonas sp. 4L, 10L and 11L showed desirable enzymatic capacities from an agrobiotechnological approach. Additionally, Pseudomonas sp. 4L increased germination and seedling growth of maize, by increasing 20–51% the number of germinated seeds, 16–38% the length of seedling aerial part, 30–140% seedling length of roots, 15–32% seedling fresh weight, and 21–33% seedling dry weight, and reduced 75–96% the damage generated by Fusarium spp. on naturally infected seeds. This study revealed that Pseudomonas sp. 4L and 11L are regional promising ecofriendly and cost-effective alternatives as adjuvants in the nutritional and phytosanitary management at seed germination and seedling growth of maize crop in Los Altos de Jalisco region, and highlight the importance of the rhizosphere microbiome of Mexican maize landrace as natural reservoir of plant growth-promoting microorganisms.

Source and Route of Pyrrolizidine Alkaloid Contamination in Tea Samples.

Toxic pyrrolizidine alkaloids (PAs) are found in tea samples, which pose a threat to human health. However, the source and route of PA contamination in tea samples have remained unclear. In this work, an adsorbent method combined with UPLC-MS/MS was developed to determine 15 PAs in the weed Ageratum conyzoides L., A. conyzoides rhizospheric soil, fresh tea leaves, and dried tea samples. The average recoveries ranged from 78%-111%, with relative standard deviations of 0.33%-14.8%. Fifteen pairs of A. conyzoides and A. conyzoides rhizospheric soilsamples and 60 fresh tea leaf samples were collected from the Jinzhai tea garden in Anhui Province, China, and analyzed for the 15 PAs. Not all 15 PAs were detected in fresh tea leaves, except for intermedine-N-oxide (ImNO) and senecionine (Sn). The content of ImNO (34.7 µg/kg) was greater than that of Sn (9.69 µg/kg). In addition, both ImNO and Sn were concentrated in the young leaves of the tea plant, while their content was lower in the old leaves. The results indicated that the PAs in tea were transferred through the path of PA-producing weeds-soil-fresh tea leaves in tea gardens.

Effects of Two Kinds of Commercial Organic Fertilizers on Growth and Rhizosphere Soil Properties of Corn on New Reclamation Land.

Due to the development of urbanization and industrialization, a large amount of cultivated land resources has been occupied, while new reclamation land could expand the supply of usable land for food security. Organic fertilizers, such as crop residues, biosolids, sheep manure, mushroom residue, and biogas liquid, have been considered as an effective amendment in immature soil to improve its quality. Recently, two kinds of commercial organic fertilizers, pig manure and mushroom residue organic fertilizer (PMMR-OF), and sheep manure organic fertilizer (SM-OF), have been more regularly applied in agriculture production. However, the information available on effect of the two kinds of fertilizers on plant growth and rhizosphere soil properties in immature field is very limited. In order to evaluate PMMR-OF and SM-OF on immature soil, the soil quality and microbial community structure of corn rhizosphere soil samples under the two kinds of organic fertilizers at different concentrations was investigated. The results revealed a significant difference between commercial organic fertilizers (especially SM-OF) and chemical compound fertilizers (CCF) in soil properties and microbial community structure. Indeed, compared with the control based on16S and ITS amplicon sequencing of soil microflora, SM-OF caused a 10.79–19.52%, 4.33–4.39%,and 14.58–29.29% increase in Proteobacteria, Actinobacteria, and Ascomycota, but a 5.82–20.58%, 0.53–24.06%, 10.87–16.79%, 2.69–10.50%, 44.90–59.24%, 8.88–10.98%, and 2.31–21.98% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Mortierellomycota, and Chytridiomycota, respectively. CCF caused a 24.11%, 23.28%, 38.87%, 19.88%, 18.28%, and 13.89% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Chytridiomycota, but a 22.77%, 41.28%, 7.88%, and 19.39% increase in Proteobacteria, Actinobacteria, Ascomycota, and Mortierellomycota, respectively. Furthermore, redundancy discriminant analysis of microbial communities and soil properties of PMMR-OF, SM-OF, CCF, and the control treatments indicated that the main variables of bacterial and fungal communities included organic matter content, available P, and available K. Overall, the results of this study revealed significant changes under different fertilizer conditions (PMMR-OF, SM-OF, CCF, under different concentrations) in microbiota and chemical properties of corn soil. Commercial organic fertilizers, particularly SM-OF, can be used as a good amendment for the new reclamation land.

Changes in rhizosphere phosphorus fractions and phosphate-mineralizing microbial populations in acid soil as influenced by organic acid exudation

Interactions were explored between organic acids, phosphate-mineralizing microorganisms, and phosphorus fractions in rhizosphere soil. Bulk soil, rhizosphere soil, and root samples were randomly collected from a mature lemon tree plantation. Composition of acid (phoC) and alkaline (phoD) phosphatase gene harboring bacterial populations in rhizosphere soil were different. Whereas only soil properties affected the phoC-harboring bacterial population, soil properties and organic acids shaped the phoD-harboring bacterial population. Organic acids, especially oxalic acid, rather than phosphatase significantly directly and indirectly affected phosphorus fractions. When oxalic acid concentration increased, abundances of phoD-harboring Pseudomonas and Bacillus also increased. Those genera then released alkaline phosphatase, which reduced the contents of calcium-bound organophosphorus, insoluble organophosphorus, and residual phosphorus. By contrast, when oxalic acid concentration decreased, abundance of phoC-harboring Xanthomonas increased. The genus released acid phosphatase, which reduced calcium-bound organophosphorus content. In addition, alkaline phosphatase released by phoD-harboring bacteria was more important than acid phosphatase in acid soil. In conclusion, oxalic acids have essential roles in directly and indirectly changing phosphorus fractions in lemon tree rhizosphere soil.

Effects of Mycorrhiza Doses and Manure Types on Growth and Yield of Cassava in Gunungkidul

Gunungkidul is a production center of cassava (Manihot esculenta Crantz), a carbohydrate source and raw material for food industry. AMF inoculation in cassava plants is known to increase biomass production. However, little studies have been conducted on the response of cassava to mycorrhizal inoculation and organic fertilizer. Therefore, this study was aimed at examining the effects of AMF inoculation and types of manure on the AMF colonization and yield of cassava in Gunungkidul. The research was carried out by planting cassava in Alfisol Gunungkidul arranged in a randomized complete block design with two factors, AMF doses of 25g; 50; and 75g/plant; and types of manure i.e. cow, goat, and poultry manure, for five months period. Rhizosphere soil and root samples were analyzed for AMF colonization and the spores number. The results showed that AMF-infected cassava roots combined with cow or goat manure application produced more spores than poultry manure. AMF infection and manure, thus, significantly resulted in better root proliferation, root forehead weight, tuber diameter, and cassava products, than the absence of both treatments. Cow manure combined with AMF at a dose of 25 g/plant significantly affected the dry weight of cassava roots. This study implies that applying AMF and manure provide a substantial contribution on the growth and production of cassava.

Soil conditions on bacterial wilt disease affect bacterial and fungal assemblage in the rhizosphere

Natural soil has the ability to suppress the soil-borne pathogen to a certain extent, and the assemblage of soil microbiome plays a crucial role in maintaining such ability. Long-term monoculture accelerates the forms of soil microbiome and leads to either disease conducive or suppressive soils. Here, we explored the impact of soil conditions on bacterial wilt disease (healthy or diseased) under long-term tobacco monoculture on the assemblage of bacterial and fungal communities in bulk and rhizosphere soils during the growth periods. With Illumina sequencing, we compared the bacterial and fungal composition of soil samples from tobacco bacterial wilt diseased fields and healthy fields in three growth periods. We found that Proteobacteria and Ascomycota were the most abundant phylum for bacteria and fungi, respectively. Factors of soil conditions and tobacco growth periods can significantly influence the microbial composition in bulk soil samples, while the factor of soil conditions mainly determined the microbial composition in rhizosphere soil samples. Next, rhizosphere samples were further analyzed with LEfSe to determine the discriminative taxa affected by the factor of soil conditions. For bacteria, the genus Ralstonia was found in the diseased soils, whereas the genus Flavobacterium was the only shared taxon in healthy soils; for fungi, the genus Chaetomium was the most significant taxon in healthy soils. Besides, network analysis confirmed that the topologies of networks of healthy soils were higher than that of diseased soils. Together, our results suggest that microbial assemblage in the rhizosphere will be largely affected by soil conditions especially after long-term monoculture.

The Effects of Secondary Growth of Spartina alterniflora after Treatment on Sediment Microorganisms in the Yellow River Delta.

As a typical invasive species, Spartina alterniflora is widely recognized as one of the primary threats to biodiversity in various habitats, including wetlands. Although the invasion by S. alterniflora has been managed in multiple ways, it may reappear after treatment. How S. alterniflora affects the soil microbial community in coastal wetlands during its regeneration process has not yet been clarified. Here, rhizosphere soil samples (RSPs) and bulk soil samples (SSPs) were collected in the S. alterniflora community and a high-throughput sequencing method was conducted to analyze the composition and diversity of soil microorganisms. Meanwhile, we also obtain the soil physicochemical properties. In the present study, there was no significant difference in the alpha diversity of both bacterial and fungal communities in the SSP and RSP groups. The PCoA (principal coordinate analysis) also showed that the microbial community structure did not differ significantly between the SSP and RSP groups. The results showed that except for pH, the total sulfur (TS) content, total nitrogen (TN) content, and electrical conductivity (EC) did not differ significantly (p > 0.05) between the SSP and RSP groups. The composition of the bacterial and fungal community in the rhizosphere of S. alterniflora was similar to that found in the surrounding soils. The top two dominant bacterial phyla were Proteobacteria and Desulfobacterota in the present study. Venn diagram results also support this view; most OTUs belong to the common OTUs of the two groups, and the proportion of unique OTUs is relatively small. The LEfSe (LDA effect size) analysis showed that Campylobacterota (at the phylum level) and Sulfurimonas (at the genus level) significantly increased in the RSP group, implying that the increased Sulfurimonas might play an essential role in the invasion by S. alterniflora during the under-water period. Overall, these results suggest that the bacterial and fungal communities were not significantly affected by the S. alterniflora invasion due to the short invasion time.

Detection of Phytophthora cinnamomi on declining Araucaria araucana forests

AbstractSince 2016, crown death and mortality of Araucaria araucana trees have been observed at different localities of the Nahuelbuta Coastal Range, Chile. The objective of this study was to determine the presence of Phytophthora spp. in the rhizosphere of A. araucana trees that may explain its decline. Samples of soil rhizosphere were collected from trees with crown death as well as from asymptomatic trees at two visually contrasting severity areas. Phytophthora detection from soil samples was carried out using leaf bait technique, and isolates were identified by morphology and molecular methods. Recovered Phytophthora isolates were used in pathogenicity tests with A. araucana plants. From rhizosphere soil samples of 30 A. araucana trees, 56 isolates of Phytophthora cinnamomi were obtained. Isolations were more frequent in the rhizosphere of trees with severe crown symptoms and originated exclusively from the selected area showing severe crown symptoms. Plant stem inoculation with P. cinnamomi isolates caused 100% mortality; however, through root infestation, mortality was variable depending on the specific isolate. These results are the first report of the pathogenicity of P.cinnamomi A2 in natural forests of A. araucana in Chile.