scholarly journals Difficult-to-culture bacteria in the rhizosphere: The underexplored signature microbial groups

Pedosphere ◽  
2022 ◽  
Vol 32 (1) ◽  
pp. 75-89
Author(s):  
Sadaf KALAM ◽  
Anirban BASU ◽  
Appa Rao PODILE
Keyword(s):  
2003 ◽  
Vol 3 (4) ◽  
pp. 145-152 ◽  
Author(s):  
H. Heinonen-Tanski ◽  
P. Juntunen ◽  
R. Rajala ◽  
E. Haume ◽  
A. Niemelä

Municipal treated wastewater has been tertiary treated in a pilot-scale rapid sand filter. The filtration process was improved by using polyaluminium coagulants. The sand-filtered water was further treated with one or two UV reactors. The quality changes of wastewater were measured with transmittance, total phosphorus, soluble phosphorus, and somatic coliphages, FRNA-coliphages, FC, enterococci and fecal clostridia. Sand filtration alone without coagulants improved slightly some physico-chemical parameters and it had almost no effect on content of microorganisms. If coagulants were used, the filtration was more effective. The reductions were 88-98% for microbial groups and 80% for total phosphorus. The wastewater would meet the requirements for bathing waters (2,000 FC/100 ml, EU, 1976). UV further improved the hygiene level; this type of treated wastewater could be used for unrestricted irrigation (2.2 TC/100 ml, US.EPA 1992). The improvement was better if coagulants were used. The price for tertiary treatment (filtration + UV) would have been 0.036 Euro/m3 according to prices in 2001 in 22 Mm3/a. The investment cost needed for the filtration unit was 0.020 Euro/m3 (6%/15a). Filtration with coagulants is recommended in spite of its costs, since the low transmittance of unfiltered wastewater impairs the efficiency of the UV treatment.


Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 222
Author(s):  
Kenji Yamane ◽  
Yuuki Kimura ◽  
Keita Takahashi ◽  
Isamu Maeda ◽  
Masayuki Iigo ◽  
...  

Aquaponics is a circulating and sustainable system that combines aquaculture and hydroponics and forms a symbiotic relationship between fish, plants, and microorganisms. We hypothesized that feed alone could support plant growth, but the symbiosis with fish adds some beneficial effects on plant growth in aquaponics. In this study, we created three closed culture systems, namely, aquaponics, hydroponics without nitrogen (N) and phosphorus (P), and aquaculture, and added the same amount of feed containing N and P to all the treatments in order to test the hypothesis. Accumulation of NO3− and PO43− was alleviated in aquaponics and hydroponics as a result of plant uptake. Lettuce plants grown in aquaponics grew vigorously until 2 weeks and contained a constant level of N in plants throughout the production period, whereas those in hydroponics grew slowly in the early stage and then vigorously after 2 weeks with a late increment of N concentration. These results suggest that catfish help with the faster decomposition of the feed, but, in hydroponics, feed can be slowly dissolved and decomposed owing to the absence of the fish. The bacterial community structures of the culture solution were investigated using 16S rRNA gene amplicon sequencing. At the class level, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the major microbial groups in the solutions. Aquaponics prevented the pollution of tank solution and maintained a higher water quality compared with hydroponics and aquaculture, suggesting that aquaponics is a more sustainable cultivation system even in a small-scale system.


2021 ◽  
Vol 9 (2) ◽  
pp. 211
Author(s):  
Jie Gao ◽  
Miao Liu ◽  
Sixue Shi ◽  
Ying Liu ◽  
Yu Duan ◽  
...  

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.


2006 ◽  
Vol 72 (10) ◽  
pp. 6452-6460 ◽  
Author(s):  
Paul J. Hunter ◽  
Geoff M. Petch ◽  
Leo A. Calvo-Bado ◽  
Tim R. Pettitt ◽  
Nick R. Parsons ◽  
...  

ABSTRACT The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.


2017 ◽  
Vol 43 (3) ◽  
pp. 53-60 ◽  
Author(s):  
Piotr Świątczak ◽  
Agnieszka Cydzik-Kwiatkowska ◽  
Paulina Rusanowska

AbstractAnaerobic digestion is an important technology for the bio-based economy. The stability of the process is crucial for its successful implementation and depends on the structure and functional stability of the microbial community. In this study, the total microbial community was analyzed during mesophilic fermentation of sewage sludge in full-scale digesters.The digesters operated at 34–35°C, and a mixture of primary and excess sludge at a ratio of 2:1 was added to the digesters at 550 m3/d, for a sludge load of 0.054 m3/(m3·d). The amount and composition of biogas were determined. The microbial structure of the biomass from the digesters was investigated with use of next-generation sequencing.The percentage of methanogens in the biomass reached 21%, resulting in high quality biogas (over 61% methane content). The abundance of syntrophic bacteria was 4.47%, and stable methane production occurred at a Methanomicrobia to Synergistia ratio of 4.6:1.0. The two most numerous genera of methanogens (about 11% total) wereMethanosaetaandMethanolinea, indicating that, at the low substrate loading in the digester, the acetoclastic and hydrogenotrophic paths of methane production were equally important. The high abundance of the orderBacteroidetes, including the classCytophagia(11.6% of all sequences), indicated the high potential of the biomass for efficient degradation of lignocellulitic substances, and for degradation of protein and amino acids to acetate and ammonia.This study sheds light on the ecology of microbial groups that are involved in mesophilic fermentation in mature, stably-performing microbiota in full-scale reactors fed with sewage sludge under low substrate loading.


2019 ◽  
Vol 121 (2) ◽  
pp. 400-410 ◽  
Author(s):  
Rinaldo Botondi

PurposeThe purpose of this paper is to evaluate the possible microbiological contamination in terms of total counts and representative microbial groups found in the hazelnuts as well as in work areas and on the working surfaces of a hazelnut processing plant.Design/methodology/approachSome microbiological parameters related to the manufacturing process (e.g. aerobic colony count yeast and fungi) were evaluated. Indoor air samples were tested in order to evaluate the possible contamination of fungal strains (i.e. mycotoxin producing fungi).FindingsThe results showed that the highest values (>of 500 CFU/m3) for bacteria and fungi were only observed in the shelling and sorting areas. Some species such as Aspergillus and Penicillium (potential mycotoxin-producers) as well as some noxious colonies ofAspergillus fumigatuswere detected along the processing line. No occurrence of aflatoxins was observed in the finished product. Microbial loads obtained through surface analyses were in accordance to the reference data.Originality/valueThe aim of this study was to monitor and improve the procedures currently used in a hazelnut processing plant.


2020 ◽  
Vol 367 (11) ◽  
Author(s):  
Andrea Fasolo ◽  
Laura Treu ◽  
Piergiorgio Stevanato ◽  
Giuseppe Concheri ◽  
Stefano Campanaro ◽  
...  

ABSTRACT Microbial metabarcoding is the standard approach to assess communities’ diversity. However reports are often limited to simple OTU abundances for each phylum, giving rather one-dimensional views of microbial assemblages, overlooking other accessible aspects. The first is masked by databases incompleteness; OTU picking involves clustering at 97% (near-species) sequence identity, but different OTUs regularly end up under a same taxon name. When expressing diversity as number of obtained taxonomical names, a large portion of the real diversity lying within the data remains underestimated. Using the 16S sequencing results of an environmental transect across a gradient of 17 coastal habitats we first extracted the number of OTUs hidden under the same name. Further, we observed which was the deepest rank yielded by annotation, revealing for which microbial groups are we missing most knowledge. Data were then used to infer an evolutionary aspect: what is, in each phylum the success of the present time individuals (abundances for each OTU) in relation to their prior evolutionary success in differentiation (number of OTUs). This information reveals whether the past speciation/diversification force is matched by the present competitiveness in reproduction/persistence. The final layer explored is functional diversity, i.e. abundances of groups involved in specific environmental processes.


2016 ◽  
Vol 113 (49) ◽  
pp. E7927-E7936 ◽  
Author(s):  
Maggie C. Y. Lau ◽  
Thomas L. Kieft ◽  
Olukayode Kuloyo ◽  
Borja Linage-Alvarez ◽  
Esta van Heerden ◽  
...  

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.


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