Influence of Soil Characteristics on the Diversity of Bacteria in the Southern Brazilian Atlantic Forest

Faoro, Helisson; Alves, Alexessander Couto; Souza, Emanuel M.; Rigo, L. U.; Cruz, Leonardo M.; Al-Janabi, Salah M.; Monteiro, Rose A.; Baura, Valter A.; Pedrosa, Fábio O.

doi:10.1128/aem.03025-09

Cited by 174 publications

(108 citation statements)

References 35 publications

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“…Specifically, the concentrations of aluminum were strongly related to the abundance of members within the family Chitinophagaceae. Aluminum has been previously shown to affect the diversity of bacteria in agricultural soils (37) and to be linked to changes in bacterial diversity in forest ecosystems (38). However, it is important that the concentrations of aluminum were correlated with the concentrations of several other heavy metals (Table S3).…”

Section: Discussionmentioning

confidence: 98%

Bacteria as Emerging Indicators of Soil Condition

Hermans

Buckley

Case

et al. 2017

Appl Environ Microbiol

217

131

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Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCEThe impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.

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Section: Discussionmentioning

confidence: 98%

Bacteria as Emerging Indicators of Soil Condition

Hermans

Buckley

Case

et al. 2017

Appl Environ Microbiol

217

131

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“…Determination of the stereochemistry of the glycerol moieties in these molecules revealed that they must derive from Bacteria (50), possibly Acidobacteria (49). The natural 13 C abundance of these bacterial tetraethers in soil is consistent with a heterotrophic lifestyle of its source organism(s) (53). Examination of a suite of bacterial cultures, including a few acidobacterial strains, for the bacterial tetraethers did not reveal their origin (49).…”

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confidence: 83%

13,16-Dimethyl Octacosanedioic Acid ( iso -Diabolic Acid), a Common Membrane-Spanning Lipid of Acidobacteria Subdivisions 1 and 3

Damsté

Rijpstra

Hopmans

et al. 2011

Appl Environ Microbiol

387

205

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The distribution of membrane lipids of 17 different strains representing 13 species of subdivisions 1 and 3 of the phylum Acidobacteria, a highly diverse phylum of the Bacteria, were examined by hydrolysis and gas chromatography-mass spectrometry (MS) and by high-performance liquid chromatography-MS of intact polar lipids. Upon both acid and base hydrolyses of total cell material, the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (iso-diabolic acid) was released in substantial amounts (22 to 43% of the total fatty acids) from all of the acidobacteria studied. This lipid has previously been encountered only in thermophilic Thermoanaerobacter species but bears a structural resemblance to the alkyl chains of bacterial glycerol dialkyl glycerol tetraethers (GDGTs) that occur ubiquitously in peat and soil and are suspected to be produced by acidobacteria. As reported previously, most species also contained iso-C 15 and C 16:17C as major fatty acids but the presence of iso-diabolic acid was unnoticed in previous studies, most probably because the complex lipid that contained this moiety was not extractable from the cells; it could only be released by hydrolysis. Direct analysis of intact polar lipids in the Bligh-Dyer extract of three acidobacterial strains, indeed, did not reveal any membrane-spanning lipids containing iso-diabolic acid. In 3 of the 17 strains, ether-bound iso-diabolic acid was detected after hydrolysis of the cells, including one branched GDGT containing iso-diabolic acid-derived alkyl chains. Since the GDGT distribution in soils is much more complex, branched GDGTs in soil likely also originate from other (acido)bacteria capable of biosynthesizing these components.

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“…Percent soil moisture (⍜) was determined gravimetrically after oven drying. Soil pH was determined by combining 10 g soil with 10 ml deionized H 2 O. Nitrogen and carbon content were determined by using dry combustion on a Carlo-Erba C/N analyzer, and phosphorus (6,14), alpine hyper arid soils (9), hot desert (8,39,47), alpine tundra (37), Antarctic peninsula/coastal (6, 45), semiarid soils (1, 26, 32), prairies/grasslands (12, 41), pasture (22), crop agriculture (7,22,29,41,50), temperate forest (17,22,29,30,41), tropical forest (13), moist acidic tundra (5), and freshwater sediments (27,48 . Fibrobacter succinogenes was used as an outgroup.…”

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confidence: 99%