Chapter 8 Microbial indicators

Impact of anthropogenic land uses on soil microbiological activity in a peri-urban landscape

Land use and land cover patterns impact soil properties and negatively affect soil microbial community and related processes. However, the information regarding the influence of urban land use on soil microbial composition and functioning is limited. Here, we investigated the impact of urban land use patterns on soil microbiological parameters by comparing five contrasting anthropogenic land use classes, i.e. agriculture, park, roadside plantation, street green, and bare land. Soil physicochemical properties, basal respiration (BR), microbial biomass carbon (MBC), and enzyme activities were estimated and correlated. The results revealed that soil physicochemical and microbiological properties greatly varied across the five land use classes. Among all the land use types, the roadside plantation had the highest nutrient content, i.e. soil organic carbon (SOC), total nitrogen (TN), and mineral nitrogen (MN) (1.33%, 0.13%, 84.0 mg kg-1, respectively), while the soil functional capacities measured in terms of BR, MBC, microbial quotient (QCO2), soil microbial activity (SMA), and dehydrogenase activity (DHA) (9.90 C µg g-1 h-1, 300 µg g-1, 0.045 µg h-1/ µg MBC, 9.0 µg ml-1, 1.30 TPF g-1 h-1, respectively) were highest in the park. Disturbed street greens were markedly nutrient depleted and apparently exhibited lower microbial activity. Variations in soil BR, MBC, and enzyme activity were revealed to be primarily influenced by soil moisture, available phosphorus, and SOC content. We concluded that the negative impacts of anthropogenic land use soil quality and microbiological functioning can be managed by integrating proper management approaches for various land use classes in urban systems.

Phytoremediation of soil contaminated with nickel, cadmium and cobalt

This pot experiment analyzed the use of Brassica napus, Elymus elongatus and Zea mays in the removal of Cd²⁺ Co²⁺ and Ni²⁺ from the soil. The utility of the plants under study for phytoremediation was analyzed based on the biomass of the aboveground parts and roots and the accumulation of metals, bioaccumulation, bioconcentration and translocation capability in the above-ground parts and roots. The effect of heavy metals on the soil enzyme activity and soil physicochemical properties was also determined. Among the species under study, only E. elongatus was found to be suitable for Cd²⁺ phytoextraction, whereas E. elongatus and Z. mays proved to be suitable for phytostabilisation of Cd²⁺ and Co²⁺ because the criterion of the accumulation of metals in the roots at a sufficient level was fulfilled. The index of bioaccumulation in roots was greater than one. Both plant species met the second condition which determined the utility for phytostabilisation, as since the transport of Cd²⁺ Co²⁺ and Ni²⁺ from the roots to the above-ground parts was limited.

Mapping Soil Biodiversity in Europe and the Netherlands

Soil is fundamental for the functioning of terrestrial ecosystems, but our knowledge about soil organisms and the habitat they provide (shortly: Soil biodiversity) is poorly developed. For instance, the European Atlas of Soil Biodiversity and the Global Soil Biodiversity Atlas contain maps with rather coarse information on soil biodiversity. This paper presents a methodology to map soil biodiversity with limited data and models. Two issues were addressed. First, the lack of consensus to quantify the soil biodiversity function and second, the limited data to represent large areas. For the later issue, we applied a digital soil mapping (DSM) approach at the scale of the Netherlands and Europe. Data of five groups of soil organisms (earthworms, enchytraeids, micro-arthropods, nematodes, and micro-organisms) in the Netherlands were linked to soil habitat predictors (chemical soil attributes) in a regression analysis. High-resolution maps with soil characteristics were then used together with a model for the soil biodiversity function with equal weights for each group of organisms. To predict soil biodiversity at the scale of Europe, data for soil biological (earthworms and bacteria) and chemical (pH, soil organic matter, and nutrient content) attributes were used in a soil biodiversity model. Differential weights were assigned to the soil attributes after consulting a group of scientists. The issue of reducing uncertainty in soil biodiversity modelling and mapping by the use of data from biological soil attributes is discussed. Considering the importance of soil biodiversity to support the delivery of ecosystem services, the ability to create maps illustrating an aggregate measure of soil biodiversity is a key to future environmental policymaking, optimizing land use, and land management decision support taking into account the loss and gains on soil biodiversity.

Mercury behaviour and C, N, and P biogeochemical cycles during ecological restoration processes of old mining sites in French Guiana

Several decades of gold mining extraction activities in the Amazonian rainforest have caused deforestation and pollution. While ecological rehabilitation is essential for restoring biodiversity and decreasing erosion on deforested lands, few studies note the behaviour or toxicity of trace elements during the rehabilitation process. Our original study focused on the potential use of microbial activity and Hg speciation and compared them with As, Cu, Zn and Cr speciation in assessing the chemical and biological quality of ecological restoration efforts. We sampled two sites in French Guyana 17 years after rehabilitation efforts began. The former site was actively regenerated (R) with the leguminous species Clitoria racemosa and Acacia mangium, and the second site was passively regenerated with spontaneous vegetation (Sv). We also sampled soil from a control site without a history of gold mining (F). We performed microcosm soil experiments for 30 days, where trace element speciation and enzyme activities (i.e., FDA, dehydrogenase, β-glucosidase, urease, alkaline and acid phosphatase) were estimated to characterise the behaviour of trace elements and the soil microbial activity. As bioindicators, the use of soil microbial carbon biomass and soil enzyme activities related to the carbon and phosphorus cycles seems to be relevant for assessing soil quality in rehabilitated and regenerated old mining sites. Our results showed that restoration with leguminous species had a positive effect on soil chemical quality and on soil microbial bioindicators, with activities that tended toward natural non-degraded soil (F). Active restoration processes also had a positive effect on Hg speciation by reducing its mobility. While in Sv we found more exchangeable and soluble mercury, in regenerated sites, Hg was mostly bound to organic matter. These results also suggested that enzyme activities and mercury cycles are sensitive to land restoration and must be considered when evaluating the efficiency of restoration processes.

Tolerance and growth kinetics of bacteria isolated from gold and gemstone mining sites in response to heavy metal concentrations

Response and growth kinetics of microbes in contaminated medium are useful indices for the screening and selection of tolerant species for eco-friendly bio-augmentative remediation of polluted environments. In this study, the heavy metal (HM) tolerance, bioaccumulation and growth kinetics of seven bacterial strains isolated from mining sites to 10 HMs (Cd, Hg, Ni, Al, Cr, Pb, Cu, Fe, Mn and Zn) at varied concentrations (25-600 mgL^-1) were investigated. The isolates were phylogenetically (16S rRNA gene) related to Lysinibacillus macroides, Achromobacter spanius, Bacillus kochii, B. cereus, Klebsiella pneumoniae, Pseudomonas mosselii and P. nitroreducens. Metal tolerance, effects on lag phase duration and growth rates were assessed using the 96-well micro-titre method. Furthermore, metal bioaccumulation and quantities within cells were determined by transmission electron microscopy and electron dispersive x-ray analyses. Tolerance to Ni, Pb, Fe and Mn occurred at highest concentrations tested. Growth rates increased with increasing Fe concentrations, but reduced significantly (p < .05) with increasing Zn, Cu, Hg, Cd and Al. Significantly higher (p < .05) growth rates (compared to controls) was found with some isolates in Hg (25 mgL^-1), Ni (100 mgL^-1), Cr (150 mgL^-1), Mn (600 mgL^-1), Pb (100 mgL^-1), Fe (600 mgL^-1) and Al (50 mgL^-1). Lag phase urations were isolate- and heavy metal-specific, in direct proportion to concentrations. A. spanius accumulated the most Mn and Zn, while B. cereus accumulated the most Cu. Metals accumulated intra-cellularly without cell morphology distortions. The isolates' multi-metal tolerance, intra-cellular metal bioaccumulation and growth kinetics suggest potentials for application in the synergetic biodegradation and bioremediation of polluted environments, especially HM-rich sites.

Soil microbial community toxic response to atrazine and its residues under atrazine and lead contamination

Intensive use of atrazine and extensive dispersal of lead (Pb) have occurred in farmland with chemical agriculture development. However, the toxicological effect of their presence on soil microorganism remains unknown. The objective of this study was to investigate the impacts of atrazine or Pb on the soil microbiota, soil net nitrogen mineralization, and atrazine residues over a 28-day microcosm incubation. The Shannon-Wiener diversity index, typical microbe species, and a Neighbor-joining tree of typical species from sequencing denaturing gradient gel electrophoresis (DGGE) bands were determined across periodical sampling times. The results showed that the existence of atrazine or Pb (especially high concentration) in soils reduced microbial diversity (the lowest H value is 2.23) compared to the control (H = 2.59) after a 28-day incubation. The species richness reduced little (from 17~19 species to 16~17 species) over the research time. But soil microbial community was significantly affected by the incubation time after the exposure to atrazine or Pb. The combination of atrazine and Pb had a significant inhibition effect on soil net nitrogen nitrification. Atrazine and Pb significantly stimulated soil cumulative net nitrogen mineralization and nitrification. Pb (300 and 600 mg kg(-1)) accelerated the level of atrazine dissipation. The exposure might stimulate the significant growth of the autochthonous soil degraders which may use atrazine as C source and accelerate the dissipation of atrazine in soils.

Bacterial diversity in agricultural soils during litter decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.