Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits

Abstract

dThis study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03-to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity. Determining the drivers of microbial community composition in soils is challenging, because soils are complex ecosystems containing numerous ecological niches. This results in an immense diversity, with up to thousands of taxa per gram of soil (1). Land use, climate, vegetation, soil type, and anthropogenic pollution are strongly linked to soil microbial community structures, functions, and activities at many sites (2-4). In particular, agricultural practices are known to drive differences in soil microbial communities (5). Influences of geogenic factors, e.g., landform, underlying lithologies, and mineral deposits on soil microbial communities, have received little attention. However, three studies of soils from Switzerland and Nepal have shown that geological/mineralogical factors can significantly affect species assemblages and functions (6-8).A primary goal of geomicrobiological research is to link microbial communities and metal cycling in metallogenic environments and to determine how communities are structured due to metalassociated drivers (9). Microorganisms play a pivotal role in the biogeochemical cycling of many metals, particularly those essential for cell function, e.g., Co, Cu, Fe, Mg, Mn, Mo, Na, Ni, V, W, and Zn, and those oxidized or reduced in catabolic reactions to gain metabolic energy, e.g., As, Fe, Mn, Mo, Sb, Se, Sn, Te, U, and V (10). Therefore, metal-rich environments are useful model systems allowing links between microbial taxa and geochemical parameters to be identified (11).To date, mine tailing and acid mine drainage sites have been ...

The Soil Microbiome of GLORIA Mountain Summits in the Swiss Alps

“…The strong influence of pH on bacterial communities is suggested to be due to the narrow pH ranges for optimal growth of bacteria, as opposed to the weaker influence on fungi which exhibit in general a wider pH tolerance (Rousk et al, 2010). The importance of parent material on composition of bacterial communities has already been reported for other cold ecosystems (Lazzaro et al, 2009; Larouche et al, 2012; Reith et al, 2015; Tytgat et al, 2016; Yashiro et al, 2016; Li et al, 2018). Parent material and soil pH are closely related since bedrock, soil age (years of weathering) and plant cover influence soil pH (Lazzaro et al, 2009).…”

“…Elevation-dependent effects on composition of microbial communities across mountain environments can further be confounded by parent material in alpine ecosystems (Lazzaro et al, 2009; Larouche et al, 2012; Shen et al, 2013; Reith et al, 2015). In addition, slope aspect and exposition (Zumsteg et al, 2013; Liu L. et al, 2015; Frey et al, 2016; Wu et al, 2017; Chai et al, 2018) can modify elevational patterns as soil temperatures can vary considerably over distances of only a few metres (Scherrer and Körner, 2011).…”

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline–Alkaline Soils

“…For example, the elements As, Ba, Cr, Cu, Ge, and Zn significantly contributed to the differences in prokaryotic community structures in both hypersaline sediments and saline soils. Our findings are supported by research showing that microelements, including As, Cr, Cu, and Zn, affected bacterial community structures in coastal sediments and metal-rich soils ( Quero et al, 2015 ; Reith et al, 2015 ). The combined microelements (As, Ba, Cr, Cu, Ge, and Zn) and variables (Cr and Cu) individually explained 21.28% and 6.93% of the total variation in community structures of prokaryotes and fungi ( Figure 6 ), indicating the relative importance of micronutrients in modulating prokaryotic composition.…”

“…Although some microelements are regarded as toxic to most forms of life, they regulated microbial communities in extreme conditions. For instance, they are significantly correlated with bacterial community composition in hot springs ( Jiang et al, 2016 ) and certain elements (Co, Ni, and Mn) explained variations of prokaryotic and fungal assemblages in polymetallic mining areas ( Reith et al, 2015 ). These previous studies have enriched our knowledge of microbial biogeography, but the respective reports are mainly focused on various macroelements.…”

Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil

“… 14 In Australia, high metal contents in soils overlying mineral deposits were discriminatory for a variety of bacterial taxa, including Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. 16 However, this is also true for many other environments, like oil reservoirs or contaminated groundwater what seems that genera/species within these phyla are established in many diverse environments. Also Hill et al 17 based on an analysis for a broad range of environmental samples, suggested that actinobacterial community structure seems to be selected by human and animal activities.…”