Molecular Monitoring of SRB Community Structure and Dynamics in Batch Experiments to Examine the Applicability of in situ Precipitation of Heavy Metals for Groundwater Remediation (15 pp)

Background, Aims and Scope   Sulfate-reducing bacteria (SRB) are known for their capacity to reduce and precipitate heavy metals (HM) as metal sulfides, offering the opportunity to create an in situ reactive zone for the treatment of heavy metal-contaminated groundwater, a process called in situ metal precipitation (ISMP). The applicability of the ISMP technology first has to be investigated at a laboratory scale before going into an on site application. The evaluation and optimization of the ISMP process is facilitated when physical/chemical analysis techniques are combined with molecular tools that specifically monitor the abundance, diversity and dynamics of the indigenous sulfate reducing microbial community. In this study, batch experiments were conducted in order to investigate the feasibility of ISMP as a groundwater remediation strategy for an industrial site contaminated with elevated levels of Zn, Cd, Co and Ni. Methods   The potential of different types of carbon source/ electron donor (lactate, acetate, methanol, ethanol, Hydrogen Release Compound?, molasses) to stimulate the sulfate reduction and metal precipitation activity of the naturally present (or indigenous) SRB community was explored. In addition, the effect of amending vitamin B12 and yeast extract was evaluated. The ISMP process was monitored by combining analytical analyzes of process parameters (SO42-concentration, heavy metal concentrations, pH, Eh) with molecular tools such as SRB subgroup and genus specific PCR, denaturing gradient gel electrophoresis (DGGE), and phylogenetic analysis of clone sequences, based on either the 16S rRNA or the dsr (dissimilatory sulfite reductase) gene. Results and Discussion   The efficiency of different carbon-sources to stimulate the ISMP process followed the order HRC 〉 molasses 〉 methanol 〉 lactate 〉 ethanol 〉 acetate. Within 10 weeks, the highest sulfate and metal removal efficiencies ranged from 85% to 99%. Addition of yeast extract boosted the ISMP process, whereas vitamin B12 negligibly affected SRB activity. Analysis of the sulfate reducing population by SRB subgroup and genus specific PCR demonstrated that members of the genus Desulfosporosinus dominated in all batch tests, while 16S rDNA DGGE profiles additionally revealed the presence in the microbial communities of non-sulfate reducing bacteria within the family Clostridium and the -proteobacteria. The dsrB-based DGGE profiles allowed us to assess the diversity and dynamics of the sulfate reducing community and added to a better understanding of the effects of different batch conditions on the ISMP process. Remarkably, all dsrB sequences affiliated with the dsrB gene sequence cluster found in Desulfotomaculum, which received their xenologous dsrB gene from the -proteobacteria. Conclusions   The batch experiments, which aimed at stimulating the activities of the indigenous SRB communities, demonstrated that these communities were present and that their activities could be used to obtain efficient in situ precipitation of the contaminating heavy metals. This opens the possibility to test this concept in the future as an on site demonstration as part of the groundwater strategy for the heavy metal contaminated site. Although batch setups are suitable for preliminary feasibility studies for ISMP, they do not reflect the in situ situation where sulfate and heavy metal and metalloid polluted groundwater are supplied continuously. A sulfate reducing strain JG32A was isolated from whose 16S rRNA gene affiliated with the genus Desulfosporosinus, while its dsrB gene sequence clustered with Desulfotomaculum dsrB gene sequences, which received their xenologous dsr genes from -proteobacteria. Therefore we hypothesize that the batch experiments enrich members of the Desulfosporosinus genus that possess a non-orthologous dsrB gene. Recommendation and Perspective   The next step towards an on site pilot test for ISMP will be the setup of a series of column experiments, with process conditions that are selected based on the above mentioned results. This will allow to define optimal ISMP process conditions and to test its long-term efficacy and sustainability before going into an on site bioremediation application. By applying the described molecular tools together with physical-chemical analyzes, it can be investigated whether the same SRB community is enriched and which type of C-source is most effective in promoting and sustaining its growth and sulfate-reduction activity.     

Effect of organic mulches on soil bacterial communities one year after application

The application of organic mulches as a soil cover is effective in improving the quality of soil. However, very little information is available on the effect of mulches on the soil microbial community. In this study, we investigated the effect of various organic mulches on soil dehydrogenase activity (DHA) and microbial community structures in the top 1 cm and 5 cm below the soil surface 1 year after application of the mulches. DHA was stimulated at both depths in plots mulched with grass clippings (GC), but was not significantly different from the control for the other mulch treatments. Fatty acid methyl ester (FAME) analysis and denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction-amplified 16S rDNA fragments were used to assess changes in the soil microbial community structure. Cluster analysis and principle component analysis of FAME profiles showed that only soil mulched with pine chips distinctively clustered from the other treatments. At the soil surface, bacterial DGGE profiles revealed that distinct shifts in several bacterial populations occurred in soils mulched with GC and eucalyptus yardwaste (EY), while DGGE profiles from soil at the 5 cm depth revealed no distinct changes. Changes in bacterial diversity at the soil surface under different mulches were calculated based on the number of bands in the DGGE profile using the Shannon-Weaver index of diversity ( H). Compared to the control ( H =0.9), the GC- and EY-treated soils showed slightly increased bacterial diversity, with an H of 1.1 and 1.0, respectively. These results indicate that the long-term effect of organic mulches on the soil microbial activity and community structure is highly dependent upon the type of mulch and is mostly exerted in the top few centimeters of the soil profile.     

Assessing the compaction susceptibility of South African forestry soils. II. Soil properties affecting compactibility and compressibility

Factors affecting the compaction susceptibility of South African forestry soils were assessed. Two traditional measures of compaction susceptibility were used: maximum bulk density (ρ_mbd) determined by the standard Proctor test, defined compactibility, and the compression index using a simple uni-axial test, defined compressibility. Soils were chosen from a broad range of geological and climatic regions and they varied greatly in texture (8 to 66 g 100 g⁻¹ clay) and organic matter content (0.26 to 5.77 g 100 g⁻¹ organic carbon). Soils showed a wide range in ρ_mbd values, from 1.24 to 2.00 Mg m⁻³, and this reflected the wide range of particle size distributions and organic matter contents of the soils. Very good correlations were achieved between measures of particle size distribution, particularly clay plus silt and both compactibility and compressibility. Both compactibility and compressibility were significantly correlated with loss-on-ignition (L_OI) which is a measure reflecting the combined effects of soil texture and organic matter on soil physical properties. Indices of compaction susceptibility were influenced more by particle size distribution than by organic carbon content. Clear effects of organic carbon on compaction behaviour were only evident for soils with low clay contents (< 25 g 100 g⁻¹. No clear relationship between compactibility and compressibility was found. Compactibility generally increased with decreasing clay plus silt content, whereas compressibility increased up to about 70 g 100 g⁻¹ clay plus silt before decreasing again. It is difficult to define compaction susceptibility solely in terms of indices of compactibility or compressibility particularly as there is no clear relationship between these two properties. A classification system for compaction risk assessment is presented, based on the relationship between compactibility (ρ_mbd) and L_OI, and between clay plus silt content and compressibility.     

重庆市土壤有机碳库的估算及其空间分布特征

基于重庆市第二次土壤普查的1411个土壤剖面数据，结合重庆市土壤图、土地利用现状图和行政区划图，在地理信息系统技术的支持下，对重庆市土壤有机碳密度及储量进行了估算、同时引入有机碳丰度指数这一指标，对有机碳在不同土壤、不同区域以及不同景观中的分布特征进行了分析。结果表明：重庆市20cm和100cm深度的土壤有机碳储量分别为0．27Tg和1．0Tg；20cm深度的土壤有机碳密度介于0．33～30．36kg／m^2之间．100cm深度的土壤有机碳密度介于1．27～72．69kg／m^2之间；重庆市土壤有机碳库在不同土壤、不同区域以及不同景观的分布具有高度的空间变异性，100cm深度的土壤、区域和景观有机碳丰度指数分别为0．58～1．95，0．55～1．39和0．46～1．58．与气候、植被、人类活动等因素密切相关。     

A new approach for modelling vertical stress distribution at the soil/tyre interface to predict the compaction of cultivated soils by using the PLAXIS code

Soil compaction by agricultural machines can have adverse effects on crop production and the environment. Different models based on the Finite Element Method have been proposed to calculate soil compaction intensity as a function of vehicle and soil properties. One problem when modelling soil compaction due to traffic is the estimation of vertical stress distribution at the soil surface, as the vertical stress is inhomogeneous (non-uniform) and depends on soil and tyre properties. However, uniform stress distribution at the soil/tyre interface is used to predict the compaction of cultivated soils in most FEM compaction models. We propose a new approach to numerically model vertical stress distribution perpendicular to the driving direction at the soil/tyre interface, employing the FEM models of PLAXIS code. The approach consists of a beam (characterised by its geometric dimensions and flexural rigidity) introduced at the soil surface and loaded with a uniform stress with the aim to simulate the action of a wheel at the soil surface. Different shapes of stress distribution are then obtained numerically at the soil surface by varying the flexural rigidity of the beam and the mechanical parameters of the soil. PLAXIS simulations show that the soil type (soil texture) modifies the shape of the stress distribution at the edges of the contact interface: a parabolic form is obtained for sand, whereas a U-shaped is obtained for clay. The flexural rigidity of the beam changes the shape of distribution which varies from a homogenous (uniform) to an inhomogeneous distribution (parabolic or U-shaped distribution). These results agree with the measurements of stress distributions for different soils in the literature. We compared simulations of bulk density using PLAXIS to measurement data from compaction tests on a loamy soil. The results show that simulations are improved when using a U-shaped vertical stress distribution which replaces a homogenous one. Therefore, the use of a beam (cylinder) with various flexural rigidities at the soil surface can be used to generate the appropriate distribution of vertical stress for soil compaction modelling during traffic.     

Bulk density by Proctor test as a function of texture for agricultural soils in Maputo province of Mozambique

Soil degradation processes may be of various kinds, including soil compaction. The present study was carried out with the objective of assessing the sensitivity of agricultural or recently abandoned soils in Maputo province of Mozambique to compaction. The assessment is based on the maximum of bulk density attained using the Proctor test (MBD).

In this study the soil texture is expressed by silt plus clay (S + C) or clay (C). The relations between the soil texture and MBD, and between soil texture and critical water content (CWC—soil water at which MBD is attained) were determined. Selected soils range from 10 to 74% of S + C and 9 to 60% of C.

The results suggest there is a relationship between the considered parameters, being that between S + C and MBD or CWC, the best. For MBD the relationship is represented by two quadratic equations with the boundary in between these being a S + C value of 25% and C value of 20%.

Based on the obtained results, one can conclude that the selected parameters may be a useful basis for estimation of the sensitivity to compaction of the Maputo province's soils. It is recommended that similar studies be carried out for soils under forest land and for soil of other provinces to establish the national physical degradation hazard as a function of soil parameters determined routinely and at low cost. The suggested parameters are texture and soil organic matter (SOM).     

A comparison of two methods for the isolation of free and occluded particulate organic matter

Various methods exist for the isolation of particulate organic matter (POM), one of the soil‐organic‐matter (SOM) fractions reacting most sensitive on land‐use or soil‐management changes. A combination of density separation and ultrasonic treatment allows to isolate two types of POM: (1) free POM and (2) POM occluded in soil aggregates. POM fractions are closely linked to their biochemical function for the formation and stabilization of aggregates, therefore methods using different aggregate sizes may result in different POM fractions isolated. We evaluated two physical fractionation procedures to reveal whether they yield different POM fractions with respect to amount and composition, using grassland and arable soils with sandy‐loam to sandy–clay‐loam texture and thus low macroaggregate stability. Method I used air‐dried aggregates of <2.0 mm size and a low‐energy sonication for aggregate disruption, method II used field‐moist aggregates <6.3 mm and a high‐energy–sonication procedure for aggregate disruption. POM fractions were analyzed by elemental analysis (C, N) and CPMAS ¹³C‐NMR spectroscopy. With both methods, about similar proportions of the SOM are isolated as free or occluded POM, respectively. The free‐ and occluded‐POM fractions obtained with method I are also rather similar in C and N concentration and composition as shown by ¹³C‐NMR spectroscopy. Method II isolates a free‐ and occluded‐POM fraction with significantly different C and N concentrations. NMR spectra revealed significant differences in the chemical composition of both fractions from method II, with the occluded POM having lower amounts of O‐alkyl C and higher amounts of aryl C and alkyl C than the free POM. Due to the use of larger, field‐moist aggregates with minimized sample pretreatment, two distinctly different POM fractions are isolated with method II, likely to be more closely linked to their biochemical function for the formation and stabilization of aggregates. High‐energy sonication as in method II also disrupts small microaggregates <63 µm and releases fine intraaggregate POM. This fraction seems to be a significant component of occluded POM, that allows a differentiation between free and occluded POM in sandy soils with significant microaggregation. It can be concluded, that microaggregation in arable soils with sandy texture is responsible for the storage of a more degraded occluded POM, that conversely supports the stabilization of fine microaggregates.     

Increased plant density with reduced nitrogen input can improve nitrogen use efficiency in winter wheat while maintaining grain yield

ABSTRACT

Plant density and nitrogen (N) input level have notable effects on root development, distribution in the soil profile, and in turn, N-uptake of winter wheat. Our study objectives were to identify whether a high yield can be maintained with a reduced N input by increasing plant density. Field studies were conducted during four successive seasons (2014–2015, 2015–2016, 2016–2017, and 2017–2018) using a widely planted cultivar, Tainong18. Two regimes of N fertilization (180 kg ha^?1 and 240 kg ha^?1) and three planting densities (135, 270, and 405 plants per m²) were used. Higher plant density led to increased root length density (RLD) and enhanced N uptake from the whole soil profile. The RLD in the soil profile at 0–1.2 m, 0–0.4 m, and 0.4–0.8 m decreased while in the 0.8–1.2 m layer it increased in response to reduced N input. The combined effects of higher plant density and lower N input resulted in reduced N uptake, a lower nitrogen nutrition index (NNI), unchanged grain yield, and improved N use efficiency. In conclusion, it is possible and sustainable to maintain a high wheat yield with reduced N input by increasing plant density.     

Least limiting water range: A potential indicator of changes in near-surface soil physical quality after the conversion of Brazilian Savanna into pasture

The Brazilian savanna, or “Cerrado”, is an ecosystem that originally covered more than 200 Mha in Brazil. It is estimated that about 49.5 Mha in the Cerrado are now covered with cultivated pastures, which are responsible for half of Brazilian beef production. However, soil and pasture degradation represent a threat to this productive system and to the Cerrado ecosystem itself. Thus, the objective of this research was to evaluate the least limiting water range (LLWR) as an index of near-surface soil physical quality after conversion of Brazilian savanna to continuous and short-duration grazing systems. Three sites were evaluated: native Cerrado (NC), continuous grazing (CG), and short-duration grazing (SG). Thirty soil cores (5 cm height, 5 cm diameter) were collected at each site, and used for soil bulk density, soil water retention curve, and soil penetration resistance curve determinations. The results were used for quantification of LLWR and critical bulk density (D_bc), in which LLWR equals zero. The near-surface soil physical quality, as evaluated by the LLWR, was most restrictive for potential root growth in SG. In CG, potential restriction was moderate; however, the entire soil bulk density range was below the D_bc. In NC, potential restriction was minimum. The soil structural degradation process was primarily related to the increase in stocking rates in the grazing systems. The LLWR proved to be a useful indicator of Cerrado soil physical quality, being sensitive to alterations in near-surface physical properties.     

Correlates of extinction risk and hunting pressure in gamebirds (Galliformes)

The 284 species of Galliformes are a highly threatened group of birds subject to direct exploitation for food, sport and cultural practices. The impact of hunting is often assumed to contribute to the high percentage of species (26.4%) listed as threatened with extinction in the IUCN Red List. We take a macroecological approach to examine the anthropogenic and ecological correlates of extinction risk and hunting pressure using linear and stepwise regression. Independent contrasts are analysed, as well as raw species data, to control for the potential confounding influence of phylogenetic trends. Extinction risk is found to be predicted both by the ecological factors considered (e.g., latitudinal range, body mass, elevational range, habitat use) and secondarily by human factors (e.g., human population density, total calorie intake, composition of diet). Hunting pressure itself is also predicted well for the threatened species by several of the anthropogenic and ecological variables. The study demonstrates that human variables can be used successfully to predict extinction risk, and represent an improvement upon methods which examine ecological variables alone. Furthermore, we show that individual threats can be explored using similar techniques, providing a more detailed insight into the processes leading to extinction. As applied to the Galliformes, both approaches provide evidence supporting the hypothesis that hunting pressure has contributed to the high proportion of threatened species in this group, and thus reinforce the case for urgent measures to reduce the impacts of direct exploitation upon these birds.