Bacteria in agricultural soils: Diversity, role and future perspectives

Topp, Edward

doi:10.4141/s01-065

Cited by 18 publications

(7 citation statements)

References 64 publications

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“…A bacterial species is considered to be "a collection of strains that show a high degree of overall similarity and differ considerably from related strain groups with respect to many independent characteristics" (Colwell et al 1995). This concept is relatively vague but it appears to be acceptable (Topp 2003). Thus, when applied to bacteria the functional diversity concept is a measure of the diversity of functional roles within the environment, as for example in the present study, the ability to metabolise different C sources.…”

Section: Microbial Functional Diversitymentioning

confidence: 94%

Biodiversity of indigenous tussock grassland sites in Otago, Canterbury and the central North Island of New Zealand III. Soil microorganisms

Sarathchandra

Burch²,

Sayer³

et al. 2005

Journal of the Royal Society of New Zealand

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Bacterial and fungal communities in indigenous tussock grassland soils were studied at four locations, Mt Benger and Deep Stream (Otago), Cass (Canterbury) and Tukino (central North Island). Soil samples collected from inter-tussock and tussock areas were used to enumerate total culturable bacteria (colony forming units (CFU)) as well as a number of specific groups of bacteria, fungal types and diversity, and soil microbial functional diversity. Soil microbial biomass carbon (C) and nitrogen (N) as well as extractable C and N were also determined. Fungal populations were lowest at Mt Benger while fluorescent Pseudomonas was lowest at Cass. In these indigenous soils, bacterial CFU were c. 30 times lower and fungal populations c. 10 times greater than in developed New Zealand pastoral soils. CFU of bacteria in complex media (r-strategists) were similar in magnitude to bacteria growing on weak CA medium (K-strategists). The microbial biomass C in indigenous grassland soils were also significantly greater than that found in developed pastoral soils, possibly due to dominance of fungi in indigenous soils. Microbial C and N were lower in Cass and Tukino sites compared to Mt Benger and Deep Stream sites. Microbial nitrogen was also significantly greater (P < 0.001) in inter-tussock than under tussock samples. The functional diversity of soil microbes, was significantly greater (P< 0.01) in inter-tussock samples compared to tussock samples at all sites except Mt Benger. The total microbial activity, as measured by the colour development in Biolog plates (Average Well Colour Development (AWCD)), was low in Cass soil compared to others. Eighty-three types of fungi belonging to 30 genera were recovered from the four sites. The diversity of fungi found in Otago sites was greater than in the other two sites (P < 0.001). Fusarium spp. that are often common in pastoral soils were conspicuous by their rarity in indigenous soils.

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Section: Microbial Functional Diversitymentioning

confidence: 94%

Biodiversity of indigenous tussock grassland sites in Otago, Canterbury and the central North Island of New Zealand III. Soil microorganisms

Sarathchandra

Burch²,

Sayer³

et al. 2005

Journal of the Royal Society of New Zealand

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“…Bacteria in rivers play an important role in the consumption of organic matter transported from the terrestrial environment to the ocean (Amon and Benner, 1996; Opsahl et al ., 1999; Hernes and Benner, 2002), and the make up of those communities likely has an impact on organic matter consumption (Covert and Moran, 2001). The diversity of bacteria in rivers may be especially high as they may contain mixtures of aquatic and terrestrial bacteria, including phylogenetically and metabolically diverse soil taxa (Liles et al ., 2003; Topp, 2003). Microbes from soil may be introduced into waterways by runoff (Zaitlin et al ., 2003) and mix with freshwater bacteria (Zwart et al ., 2002).…”

Section: Introductionmentioning

confidence: 99%

Bacterial diversity of metagenomic and PCR libraries from the Delaware River

Cottrell

Waidner

et al. 2005

Environmental Microbiology

121

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To determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make-up of a large insert metagenomic library constructed with bacterial DNA from the Delaware River, a polymerase chain reaction (PCR) library of 16S rRNA genes, and community structure determined by fluorescence in situ hybridization (FISH). The composition of the libraries and community structure determined by FISH differed for the major bacterial groups in the river, which included Actinobacteria, beta-proteobacteria and Cytophaga-like bacteria. Beta-proteobacteria were underrepresented in the metagenomic library compared with the PCR library and FISH, while Cytophaga-like bacteria were more abundant in the metagenomic library than in the PCR library and in the actual community according to FISH. The Delaware River libraries contained bacteria belonging to several widespread freshwater clusters, including clusters of Polynucleobacter necessarius, Rhodoferax sp. Bal47 and LD28 beta-proteobacteria, the ACK-m1 and STA2-30 clusters of Actinobacteria, and the PRD01a001B Cytophaga-like bacteria cluster. Coverage of bacteria with > 97% sequence identity was 65% and 50% for the metagenomic and PCR libraries respectively. Rarefaction analysis of replicate PCR libraries and of a library constructed with re-conditioned amplicons indicated that heteroduplex formation did not substantially impact the composition of the PCR library. This study suggests that although it may miss some bacterial groups, the metagenomic approach can sample other groups (e.g. Cytophaga-like bacteria) that are potentially underrepresented by other culture-independent approaches.

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“…The negative effects of pesticides on soil microflora are of great importance, because many microbial functions are critical to crop production, soil sustainability and environmental quality [5]. The structure and diversity of soil microbes, together with their metabolic activities, appear to be a crucial aspect within such a scenario.…”

Section: Abstract: Difenoconazole Soil Bacteriamentioning

confidence: 99%

The Effects of Difenoconazole Treatment on Microorganism from Soil

Filimon¹,

Popescu²,

Verdeş³

et al. 2018

Rev. Chim.

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The present study quantified the effect of difenoconazole (DFC) on bacteria and mold communities grown in laboratory conditions, in treated soil microcosms difenoconazole, using the following concentrations: control, half dose (0.037 mg DFC / g soil, HD), normal dose (0.075 mg DFC / g soil, ND) and double dose (0.150 mg DFC / g soil, DD). The microbiological analysis included mesophilic bacteria involved in the nitrogen cycle: aerobic and anaerobic nitrogen-fixing, ammonifying, nitrifying and denitrifying bacteria. The mesophilic bacteria were incubated at 37�C and identified qualitatively on solid growth medium (Nutrient agar), whereas soil fungi were identified both quantitatively and qualitatively on solid growth medium (Potato-Glucose-Agar). In high doses, the DFC decreased the microbial communities involved in nitrogen cycle, namely aerobic and anaerobic bacteria and denitrifying bacteria. Noticeable was the response of two genera, namely Mucor sp. and Actinomucor sp., that showed resistance to the toxic effect of DFC, underlying their potential further practical use in the decontamination of polluted soils.

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Bacteria in agricultural soils: Diversity, role and future perspectives

Cited by 18 publications

References 64 publications

Biodiversity of indigenous tussock grassland sites in Otago, Canterbury and the central North Island of New Zealand III. Soil microorganisms

Biodiversity of indigenous tussock grassland sites in Otago, Canterbury and the central North Island of New Zealand III. Soil microorganisms

Bacterial diversity of metagenomic and PCR libraries from the Delaware River

The Effects of Difenoconazole Treatment on Microorganism from Soil

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