Microbial community changes in different underground compartments of potato affected yield and quality

Soil microbial communities are critical to plant health and productivity. Crop-associated microbial diversity may exhibit spatial specificity across regions and soil compartments. However, we lack sound evidence for the impact of variation in soil microbial diversity on plant productivity caused by regional differences. The main aims of this study are to explore the structure and functionality of the belowground (potato tuber surface and rhizosphere) microbial communities in three compartments and assess whether these communities contribute to potato productivity. Significant differences in alpha and beta diversities of belowground microbiota were detected in different compartments and regions, mainly due to differences in available soil nutrients and pH. Changes to microbial diversity between bulk soil and rhizosphere or tuber surface soil were significantly negatively correlated with potato yield and nutrient content and positively correlated with starch content. We further found some bacterial (Mucilaginibacter, Dokdonella, and Salinispora) and fungal (Solicoccozyma, Scytalidium, and Humicola) genera closely associated with potato yield and quality. Aggregated boosted tree prediction revealed that soil physicochemical properties and microbial diversity of tuber surface soil contributed more to potato yield; tuber surface soil bacterial contributed more to potato starch and nutrient content. Our findings provide experimental evidence that the significant differences in soil microbial diversity and specific microbial taxa enrichment may potentially influence crop productivity under soil physicochemical property change scenarios in the agricultural ecosystem.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03167-6.

Simultaneous nitrification-denitrification (SND) using a thermoplastic gel as support: pollutants removal and microbial community in a pilot-scale biofilm membrane bioreactor

In this study, experiments were carried out to treat sanitary wastewater in a biofilm membrane bioreactor using a thermoplastic gel as a support to assist the nitrification-denitrification process. For this purpose, the system was operated in two different dissolved oxygen concentrations (2.3 ± 0.2 and 0.9 ± 0.3 mg O2/L for Phases I and II, respectively) and the removal of organic compounds and nitrogen, as well as the microbial community in suspended biomass and biofilm were evaluated. The MB-MBR system was able to withstand raw wastewater variations and maintaining a low permeate COD concentration (18 mg/L) even at low DO concentrations. On the other hand, it was found that oxygen concentration significantly influenced the process of nitrogen conversion. In Phase I the average removal of total nitrogen was 18 ± 8%, while in Phase II it increased to 66 ± 11%. The denitrification rate was two times higher (7.8 mg NO 3 - -N/h) at low dissolved oxygen, with a significant contribution of the biofilm (41%). Additionally, the high-throughput 16S rDNA sequencing showed that the oxygen concentration was determinant for arrangement patterns of the samples and not the sampling site (suspended biomass and support material). Thiothrix, Comamonas, Rhodobacter, Mycobacterium, Thermomonas, Sphingobium, Sphigopyxis, Pseudoxanthomonas, Nitrospira and, Novosphingobium were the main genera regarding the nitrogen cycle.

Substrate availability drives mixed culture fermentation of glucose to lactate at steady state

Mixed-culture fermentation (MCF) enables carbon recycling from complex organic waste streams into valuable feedstock chemicals. Using complex microbial consortia, MCF systems can be tuned to produce a range of biochemicals to meet market demand. However, the metabolic mechanisms and community interactions which drive biochemical production changes under differing conditions are currently poorly understood. These mechanisms are critical to useful MCF production models. Furthermore, predictable product transitions are currently limited to pH-driven changes between butyrate and ethanol, and chain-elongation (fed by lactate, acetate, and ethanol) to butyrate, valerate, and hexanoate. Lactate, a high-value biopolymer feedstock chemical, has been observed in transition states, but sustained production has not been described. In this study, steady state lactate production was achieved by increasing the organic loading rate of a butyrate-producing system from limiting to nonlimiting conditions at pH 5.5. Crucially, butyrate production resumed upon return to substrate-limited conditions. 16S ribosomal DNA community profiling combined with metaproteomics demonstrated that the butyrate-producing lineage Megasphaera redirected carbon flow through the methylglyoxal bypass when substrate was nonlimiting, which altered the community structure and metabolic expression toward lactate production. This metabolic mechanism can be included in future MCF models to describe the changes in product generation in substrate nonlimiting conditions.

In Situ Growth of Halophilic Bacteria in Saline Fracture Fluids from 2.4 km below Surface in the Deep Canadian Shield

Energy derived from water-rock interactions such as serpentinization and radiolysis, among others, can sustain microbial ecosystems deep within the continental crust, expanding the habitable biosphere kilometers below the earth's surface. Here, we describe a viable microbial community including sulfate-reducing microorganisms from one such subsurface lithoautotrophic ecosystem hosted in fracture waters in the Canadian Shield, 2.4 km below the surface in the Kidd Creek Observatory in Timmins, Ontario. The ancient groundwater housed in fractures in this system was previously shown to be rich in abiotically produced hydrogen, sulfate, methane, and short-chain hydrocarbons. We have further investigated this system by collecting filtered water samples and deploying sterile in situ biosampler units into boreholes to provide an attachment surface for the actively growing fraction of the microbial community. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and DNA sequencing analyses were undertaken to classify the recovered microorganisms. Moderately halophilic taxa (e.g., Marinobacter, Idiomarina, Chromohalobacter, Thiobacillus, Hyphomonas, Seohaeicola) were recovered from all sampled boreholes, and those boreholes that had previously been sealed to equilibrate with the fracture water contained taxa consistent with sulfate reduction (e.g., Desulfotomaculum) and hydrogen-driven homoacetogenesis (e.g., Fuchsiella). In contrast to this "corked" borehole that has been isolated from the mine environment for approximately 7 years at the time of sampling, we sampled additional open boreholes. The waters flowing freely from these open boreholes differ from those of the long-sealed borehole. This work complements ongoing efforts to describe the microbial diversity in fracture waters at Kidd Creek in order to better understand the processes shaping life in the deep terrestrial subsurface. In particular, this work demonstrates that anaerobic bacteria and known halophilic taxa are present and viable in the fracture waters presently outflowing from existing boreholes. Major cations and anions found in the fracture waters at the 2.4 km level of the mine are also reported.

Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

The operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.

Dokdonella koreensis bacteremia: A case report and review of the literature

Dokdonella koreensis is a recently discovered organism that was isolated from an island in Korea in 2006. The authors describe a case involving a 75-year-old man undergoing chemotherapy for acute myeloid leukemia who developed a bloodstream infection that was eventually discovered to be due to D koreensis. The authors discuss the similarities between this case and the only other reported case of infection due to D koreensis reported in the literature.

Dokdonella koreensis is a non-spore-forming, aerobic, Gram-negative bacillus that was initially isolated from soil. The pathogenicity of this organism in humans remains unclear. The authors report a case of successfully treated D koreensis bacteremia in a patient with a hematological malignancy who presented with a fever and palmar-plantar erythrodysesthesia.

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan

The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils.

Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family Xanthomonadaceae isolated from an agricultural soil, and emended description of the genus Dokdonella

A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031T was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031T formed a discrete monophyletic lineage in the family Xanthomonadaceae , sharing high pairwise sequence similarity of 93.5–95.2 and 94.8 % with species of the genus Dokdonella (94.9 % similarity to the type strain of the type species) and Aquimonas voraii GPTSA 20T, respectively. The genomic DNA G+C content of strain CC-YHH031T was 68.6±0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5 % of total fatty acids) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 1ω9c, iso-C14 : 0, iso-C11 : 0 and iso-C11 : 0 3-OH. The polar lipid profile of strain CC-YHH031T included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1–2) and four unidentified phospholipids (PL1–4). Strain CC-YHH031T was distinguished particularly from the type species of the genus Dokdonella ( Dokdonella koreensis ) by the presence of major amounts of iso-C14 : 0 and summed feature 3 and minor amounts of iso-C17 : 0 and by the complete absence of anteiso-C17 : 0, the presence of PL1–3 and APL1–2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031T is proposed to represent a novel genus and species within the family Xanthomonadaceae , for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031T ( = BCRC 80273T = DSM 24163T).

Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5T, was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5T was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5T was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16–37 °C (optimum 25 °C) and at pH 5.0–8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5T were rods that measured 0.3–0.5 µm in width and 3.0–5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5T clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123T (96.4 % sequence similarity), Dokdonella fugitiva A3T (96.1 %), Dokdonella soli KIS28-6T (95.7 %) and Dokdonella ginsengisoli Gsoil 191T (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5T was considered to represent a novel species of the genus Dokdonella , for which the name Dokdonella immobilis is proposed. The type strain is LM2-5T ( = CGMCC 1.7659T  = JCM 15763T).

Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm

A Gram-stain-negative, non-motile, facultatively anaerobic, acid-tolerant rod, designated strain DKE6T, was isolated from an acidic biofilm (pH 2.5) harvested in the pyrite mine Drei Kronen und Ehrt in Germany. The isolate grew optimally at pH 5.5, between 25 and 30 °C and only with casein as the carbon and energy source; although a variety of sugars were tested as growth substrates, none supported growth of the isolate. During casein consumption, strain DKE6T produced ammonium, which led to an alkalinization of the medium. This is a possible strategy to raise the pH in the direct vicinity of the cell and hence modulate the pH towards the growth optimum. The predominant fatty acids (>5 %) were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 66.6 %. Strain DKE6T was not able to oxidize iron or thiosulfate. Iron reduction was detected. The isolate showed 93.3 % 16S rRNA gene sequence similarity to the most closely related cultivable strain, Dokdonella koreensis DS-123T, but <93.2 % sequence similarity with other type strains of closely related type species of the Gammaproteobacteria . On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Gammaproteobacteria , for which we propose the name Metallibacterium scheffleri gen. nov., sp. nov. The type strain of the type species is DKE6T ( = DSM 24874T = JCM 17596T).

Dokdonella kunshanensis sp. nov., isolated from activated sludge, and emended description of the genus Dokdonella

A Gram-negative, aerobic, non-motile, non-spore-forming rod, designated DC-3T, was isolated from activated sludge of a wastewater treatment plant in China. Comparative 16S rRNA gene sequence analysis showed that strain DC-3T belonged to the family Xanthomonadaceae and formed a lineage within the genus Dokdonella . Strain DC-3T shared the highest 16S rRNA gene sequence similarity with Dokdonella soli KIS28-6T (97.1 %) and Dokdonella fugitiva A3T (97.1 %). The G+C content of the genomic DNA was 71.5 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17 : 1ω9c (31.6 %), iso-C15 : 0 (12.6 %), iso-C16 : 0 (21.3 %), iso-C17 : 0 (13.1 %) and iso-C11 : 0 3-OH (6.5 %), which supported the affiliation of strain DC-3T with the genus Dokdonella . DNA–DNA relatedness between strain DC-3T and its closest phylogenetic neighbours was <30 %. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain DC-3T from the recognized species of the genus Dokdonella . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain DC-3T represents a novel species of the genus Dokdonella , for which the name Dokdonella kunshanensis sp. nov. is proposed. The type strain is DC-3T ( = CCTCC AB 2011179T  = KACC 16511T). The description of the genus Dokdonella is also emended.

Arenimonas metalli sp. nov., isolated from an iron mine

A Gram-staining-negative, aerobic, rod-shaped bacterium (CF5-1T) was isolated from Hongshan Iron Mine, Daye City, Hubei province, China. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. The genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CF5-1T was most closely related to Arenimonas malthae (95.3 % gene sequence similarity), Arenimonas oryziterrae (94.7 %), Arenimonas donghaensis (94.6 %) and Arenimonas composti (94.5 %). A taxonomic study using a polyphasic approach showed that strain CF5-1T represents a novel species of the genus Arenimonas , for which the name Arenimonas metalli sp. nov. is proposed. The type strain is CF5-1T ( = CGMCC 1.10787T = KCTC 23460T = CCTCC AB 2010449T).