Low pH and aluminum tolerance of<i>Bradyrhizobium</i>strains isolated from acid soils in Indonesia

Ozawa, Tohru; Imai, Yumiko; Sukiman, Harmastini; Karsono, Herry; Ariani, Dini; Saono, Susono

doi:10.1080/00380768.1999.10414349

Cited by 6 publications

(3 citation statements)

References 14 publications

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“…On genus level, when the heterogeneity is reduced, edaphic properties like soil pH and cations (Ca and Cu) were associated with the distribution of diazotrophic genera. In detail, read abundance of the genera Calothrix and Bradyrhizobium correlated with soil pH, concordant with earlier studies isolating Calothrix strains from alkaline ( Pandey et al, 2005 ; Nayak and Prasanna, 2007 ; Rinkel and Manoylov, 2014 ) and Bradyrhizobium strains from acidic environments ( Graham et al, 1994 ; Ozawa et al, 1999 ). Although Cu is an important co-factor for enzymes, it can have a toxic effect on bacteria ( Trevors and Cotter, 1990 ; Ladomersky and Petris, 2015 ), which might explain the decrease of Bradyrhizobium read abundance.…”

Section: Discussionsupporting

confidence: 90%

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

et al. 2022

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Grassland ecosystems cover around 37% of the ice-free land surface on Earth and have critical socioeconomic importance globally. As in many terrestrial ecosystems, biological dinitrogen (N2) fixation represents an essential natural source of nitrogen (N). The ability to fix atmospheric N2 is limited to diazotrophs, a diverse guild of bacteria and archaea. To elucidate the abiotic (climatic, edaphic), biotic (vegetation), and spatial factors that govern diazotrophic community composition in global grassland soils, amplicon sequencing of the dinitrogenase reductase gene—nifH—was performed on samples from a replicated standardized nutrient [N, phosphorus (P)] addition experiment in 23 grassland sites spanning four continents. Sites harbored distinct and diverse diazotrophic communities, with most of reads assigned to diazotrophic taxa within the Alphaproteobacteria (e.g., Rhizobiales), Cyanobacteria (e.g., Nostocales), and Deltaproteobacteria (e.g., Desulforomonadales) groups. Likely because of the wide range of climatic and edaphic conditions and spatial distance among sampling sites, only a few of the taxa were present at all sites. The best model describing the variation among soil diazotrophic communities at the OTU level combined climate seasonality (temperature in the wettest quarter and precipitation in the warmest quarter) with edaphic (C:N ratio, soil texture) and vegetation factors (various perennial plant covers). Additionally, spatial variables (geographic distance) correlated with diazotrophic community variation, suggesting an interplay of environmental variables and spatial distance. The diazotrophic communities appeared to be resilient to elevated nutrient levels, as 2–4 years of chronic N and P additions had little effect on the community composition. However, it remains to be seen, whether changes in the community composition occur after exposure to long-term, chronic fertilization regimes.

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Section: Discussionsupporting

confidence: 90%

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

et al. 2022

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“…Although this phylogenetical pattern was observed for some groups of OTUs in our data, it is still hypothesized that a high degree of variation to pH exists even at species/strain levels [ 1 ] and not well resolved by 16S rRNA gene sequence-based analysis. For example, it is known that during isolation and screening of symbiotic Bradyrhizobium isolates, a wide variation of genotypes growing in different pH ranges can be found, with a generally expected predominance in neutral pH ranges [ 23 , 24 ]. In our study, Bradyrhizobium (including environmental genotypes) had higher relative occurrence in low pH, as also reported in a European soil [ 4 ].…”

Section: Discussionmentioning

confidence: 99%

“…Although overall bacterial diversity is usually also highest in this pH range [ 1 , 3 , 6 , 20 ], the optimal ranges of pH and nutrients for most environmental microorganism species are still largely unknown [ 4 , 9 , 21 ]. Some studies investigating the interaction of plants and microorganisms, such as the symbiosis between rhizobia and leguminous plants, demonstrated that Ca, P, Fe, and Mo stimulate these bacteria and that their optimal pH was also near 6 [ 11 , 22 – 24 ]. Other examples of the effects from pH-driven changes in soil nutrient availability on bacterial species or communities are summarized in Additional file 1 .…”

Section: Introductionmentioning

confidence: 99%

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

et al. 2018

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BackgroundpH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to “spillover effects” on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures.ResultsWe evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical–chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes.ConclusionsOur results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and “spillover effects” of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0482-8) contains supplementary material, which is available to authorized users.

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The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale

Lopez

Morel

Benizri

2022

Science of The Total Environment

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Low pH and aluminum tolerance ofBradyrhizobiumstrains isolated from acid soils in Indonesia

Cited by 6 publications

References 14 publications

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

Global Grassland Diazotrophic Communities Are Structured by Combined Abiotic, Biotic, and Spatial Distance Factors but Resilient to Fertilization

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale

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