The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island

An investigation of the influence of soil properties on microbial community dynamics in soil on sub-Antarctic Macquarie Island found that both carbon and nitrogen were important factors in determining soil microbial community structure. The phylogenetic diversity of soil microbial communities in hydrocarbon contaminated and non-contaminated sites was compared to the diversity of hydrocarbon-degrading genes and soil physicochemical characteristics. Genes involved in hydrocarbon degradation including alkane mono-oxygenase, catchecol-2,3-dioxygenase and naphthalene dioxygenase were found throughout the study sites. Terminal restriction fragment length polymorphism analysis of the 16S rRNA and alkB genes found that the patterns of diversity of these two genes were only correlated with each other where measurable levels of hydrocarbons were detected. We found that different sections of the microbial community are affected by different environmental factors depending on whether hydrocarbons were present. The overall microbial community structure as measured by the 16S rRNA gene was most influenced by the presence of carbon both as total organic carbon and as petroleum hydrocarbons. The alkane-degrading community was also influenced by carbon. Where hydrocarbons were present petroleum hydrocarbon concentration as well as the form and concentration of nitrogen present also influenced the alkane-degrading community. This level of complexity in the microbial community dynamics suggests that it is unlikely that one single environmental factor is responsible for structuring microbial communities.     

Regulation of bacterial and fungal MCPA degradation at the soil-litter interface

Much is known about mechanisms and regulation of phenoxy acid herbicide degradation at the organism level, whereas the effects of environmental factors on the performance of the phenoxy acid degrading communities in soils are much less clear. In a microcosm experiment we investigated the small-scale effect of litter addition on the functioning of the MCPA degrading communities. ¹⁴C labelled MCPA was applied and the functional genes tfdA and tfdAα were quantified to characterise bacterial MCPA degradation. We identify the transport of litter compounds as an important process that probably regulates the activity of the MCPA degrading community at the soil-litter interface. Two possible mechanisms can explain the increased tfdA abundance and MCPA degradation below the litter layer: 1) transport of α-ketoglutarate or its metabolic precursors reduces the costs for regenerating this co-substrate and thereby improves growth conditions for the MCPA degrading community; 2) external supply of energy and nutrients changes the internal resource allocation towards enzyme production and/or improves the activity of bacterial consortia involved in MCPA degradation. In addition, the presence of litter compounds might have induced fungal production of litter-decaying enzymes that are able to degrade MCPA as well.     

n-Alkanes and free fatty acids in humus and A1 horizons of soils under beech, spruce and grass in the Massif-Central (Mont-Lozère), France

Soil profiles under beech, spruce and a grassland have been analysed to study the evolution of natural n-alkanes in pollution-free ecosystems. The soils had all developed on granitic bedrock, at an altitude of 1300–1500 m in the region of Mont-Lozère (southern Massif-Central, France). In contrast to the grassland soil, the two forest soils both possessed a well-developed acidic moder humus-type horizon. This could be subdivided as follows: fresh litter (OL), fragmentation (OF) and humification (OH) layers; two litters, one fresh (OL1) and one old (OL2) could actually be distinguished in the beech forest soil. The n-alkane signature of the parent plants was preserved in the top litter. Immediately underneath, in the OF layer(s) the original n-alkane signatures were progressively but rapidly replaced by a common signature composed of n-C₂₇ and n-C₂₅ with larger proportions of the former than of the latter. These two hydrocarbons were most probably produced in situ by fungi. These results appear to illustrate the action of soil microorganisms which metabolize the inherited n-alkanes and produce new compounds of the same family. Unlike the alkanes and the low molecular weight fatty acids ≤ C₂₀ (which increase greatly in the OL2 layer under beech as a result of intense microbial activity), the heavy fatty acids (> C₂₀) show no significant change in the organic horizon.     

Effects of flue gas desulfurization gypsum by-products on microbial biomass and community structure in alkaline–saline soils

Purpose

For an alkaline?Csaline region in Northwest China, we examined the responses of soil microbial communities to flue gas desulfurization gypsum by-products (FGDB), a new ameliorant for alkaline?Csaline soils. In 2009 and 2010, we collected soils from 0?C20?cm and 20?C40?cm depths along an experimental FGDB gradient (0, 0.74, 1.49, 2.25, and 3.00?kg FGDB m^?2).

Materials and methods

As a measure of microbial community composition and biomass, we analyzed phospholipid fatty acids (PLFAs). We used real-time quantitative polymerase chain reaction (qPCR) to measure abundance of bacterial 16?S rRNA copy numbers. Additionally, physicochemical soil parameters were measured by common laboratory methods.

Results and discussion

Microbial community composition differed along the FGDB gradient; however, the microbial parameters did not follow a linear response. We found that, in 2009, total PLFA concentrations, and concentrations of total bacterial and Gram-negative bacterial PLFAs were slightly higher at intermediate FGDB concentrations. In 2010, total PLFA concentrations, and concentrations of total bacterial, Gram-positive bacterial, Gram-negative bacterial, and fungal PLFAs as well as the fungal:bacterial PLFA ratio were highest at 1.49?kg FGDB m^?2 and 3.00?kg FGDB m^?2. PLFA concentrations often differed between 2009 and 2010; however, the patterns varied across the gradient and across microbial groups. For both years, PLFA concentrations were generally higher at 0?C20?cm depth than at 20?C40?cm depth. Similar results were obtained for the 16?S rRNA copy numbers of bacteria at 0?C20?cm depth. FGDB addition resulted in an increase in soil Ca²⁺ and NO ₃ ^? ?CN and a decrease in pH and electrical conductivity (EC). Shifts in PLFA-based microbial community composition and biomass could partly be explained by pH, soil organic carbon, total nitrogen (TN), soil moisture, EC, inorganic nitrogen, C/N, and Ca²⁺. Indirect effects via shifts in abiotic soil properties, therefore, seem to be an important pathway through which FGDB affect soil microbial communities.

Conclusions

Our results demonstrate that addition of FGDB leads to significant changes in soil physicochemical and microbial parameters. As such, addition of FGDB can have large impacts on the functioning of soil ecosystems, such as carbon and nitrogen cycling processes.     

Compartmentalization of the soil animal food web as indicated by dual analysis of stable isotope ratios (N/N and C/C)

The soil animal food web has become a focus of recent ecological research but trophic relationships still remain enigmatic for many taxa. Analysis of stable isotope ratios of N and C provides a powerful tool for disentangling food web structure. In this study, animals, roots, soil and litter material from a temperate deciduous forest were analysed. The combined measurement of δ¹⁵N and δ¹³C provided insights into the compartmentalization of the soil animal food web. Leaf litter feeders were separated from animals relying mainly on recent belowground carbon resources and from animals feeding on older carbon. The trophic pathway of leaf litter-feeding species appears to be a dead end, presumably because leaf litter feeders (mainly diplopods and oribatid mites) are unavailable to predators due to large size and/or strong sclerotization. Endogeic earthworms that rely on older carbon also appear to exist in predator-free space. The data suggest that the largest trophic compartment constitutes of ectomycorrhizal feeders and their predators. Additionally, there is a smaller trophic compartment consisting of predators likely feeding on enchytraeids and potentially nematodes.     

脱硫废弃物改良宁夏盐渍化土壤对细菌和氨氧化微生物丰度的影响

为探明脱硫废弃物改良盐渍化土壤对微生物群落的影响效果,在2009~2010年,采用田间试验,施用不同量的脱硫废弃物(0、0.74、1.49、2.25、3.00 kg·m-2),研究了脱硫废弃物对盐渍化土壤细菌、氨氧化细菌和氨氧化古菌的影响。试验结果表明:0~20 cm土层,Ca2+和NO-3-N含量随着施用量增加而增加;土壤p H值、电导率值显著下降。实时荧光定量PCR(q PCR)分析结果表明,微生物丰度随着脱硫废弃物的施用发生变化,但这种变化并不与脱硫废弃物的施用量呈线性关系。在0~20 cm土壤层,施脱硫废弃物使得细菌16S rRNA基因拷贝数处理组显著高于对照组。氨氧化古菌与氨氧化细菌基因拷贝数在T2和T4处理高于其它处理。20~40 cm土层各处理间微生物群落没有显著变化,或没有出现规律的变化趋势。因此,脱硫废弃物增加了土壤细菌和氨氧化功能基因丰度,且对上层土壤影响更为显著。本研究中施用脱硫废弃物1.49 kg·m-2(T2)是引起细菌和氨氧化功能基因丰度增加的施用量。     

Spatial patterns of microbial denitrification genes change in response to poultry litter placement and cover crop species in an agricultural soil

Subsurface-banding manure and winter cover cropping are farming techniques designed to reduce N loss. Little is known, however, about the effects of these management tools on denitrifying microbial communities and the greenhouse gases they produce. Abundances of bacterial (16S), fungal (ITS), and denitrification genes (nirK, nirS, nosZ-I, and nosZ-II) were measured in soil samples collected from a field experiment testing the combination of cereal rye and hairy vetch cover cropping with either surface-broadcasted or subsurface-banded poultry litter. The spatial distribution of genes was mapped to identify potential denitrifier hotspots. Spatial distribution maps showed increased 16S rRNA genes around the manure band, but no denitrifier hotspots. Soil depth and nitrate concentration were the strongest drivers of gene abundance, but bacterial gene abundance also differed by gene, soil characteristics, and management methods. Gene copy number of nirK was higher under cereal rye than hairy vetch and positively associated with soil moisture, while nirS gene copies did not differ between cover crop species. The nirS gene copies increased when manure was surface broadcasted compared to subsurface banded and was positively associated with pH. Soil moisture and pH were positively correlated to nosZ-II but not to nosZ-I gene copy numbers. We observed stronger correlations between nosZ-I and nirS, and nosZ-II and nirK gene copies compared to the reverse pairings. Agricultural management practices differentially affect spatial distributions of genes coding for denitrification enzymes, leading to changes in the composition of the denitrifying community.     

Abundance and community structure of sulfate reducing prokaryotes in a paddy soil of southern China under different fertilization regimes

Flooded rice paddy soils represent a typical anaerobic freshwater habitat of microorganisms. The abundance and community structure of sulfate reducing prokaryotes (SRP) were investigated in order to understand their response to different fertilization practices in rice paddy, including control without fertilizers (CT) and arrangements of different chemical fertilizers of nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK and NPK. The abundance of total bacteria and sulfate reducing prokaryotes of the rice paddy in summer and in winter were quantified by real-time PCR assays based on the 16S rRNA gene and the dissimilatory (bi)sulfite reductase gene (dsrAB) β-subunit. No significant differences in the bacterial and SRP abundance were observed among different fertilization treatments in both winter and summer. The mean copy numbers of bacteria was 7.26 × 10⁹ copies g⁻¹ dry soil in winter and 1.27 × 10¹⁰ copies g⁻¹ dry soil in summer. The average dsrAB gene copy numbers of the SRP was 5.08 × 10⁸ copies g⁻¹ dry soil in winter and 5.92 × 10⁸ copies g⁻¹ dry soil in summer. The dsrAB gene clone libraries of the five fertilization treatments were constructed and their RFLP analysis yielded 22-25 restriction patterns, suggesting a high degree of dsrAB sequence diversity in different fertilization treatments. There was no significant change in the soil SRP community structure among the different fertilization regimes. More than half of the sequences were affiliated with novel branching clusters which were uncultured SRP. Clostridia and Deltaproteobacteria were also found with a high proportion in the clone libraries, while Desulfovibrionaceae was absent. High proportion of novel uncultured SRP implies that they may play important roles in paddy soils and deserve further studies.     

Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols

Soil pollution by elevated heavy metals exhibits adverse effects on soil microorganisms. Ammonia oxidizing bacteria and ammonia oxidizing archaea perform ammonia oxidative processes in acidic soils. However, influence of heavy metal stress on soil ammonia oxidizers distribution and diversity is inadequately addressed. This study investigated the responses of ammonia oxidizing bacteria and archaea to heavy metals, Cu and As during short-term laboratory experiment. Two different acidic alfisols named as Rayka and Hangzhou spiked with different concentrations of As, Cu and As + Cu were incubated for 10 weeks. Significant reduction in copy numbers of archaeal-16S rRNA, bacterial-16S rRNA and functional amoA genes was observed along elevated heavy metal concentrations. Ammonia oxidizing archaea was found to be more abundant than ammonia oxidizing bacteria in all the heavy metal treatments. The potential nitrification rate significantly decreased with increasing As and Cu concentrations in the two soils examined. Denaturing gradient gel electrophoresis analysis revealed no apparent community shift for ammonia oxidizing archaea even at higher concentrations of As and Cu. Phylogenetic analysis of archaeal amoA gene from 4 clone libraries indicated that all the archaeal amoA sequences were placed within 3 distinct clusters from soil and sediment group 1.1b of Thaumarchaeota. Our results could be useful for the better understanding of the ecological effects of heavy metals on the abundance and diversity of soil ammonia oxidizers.     

Diversity, abundance and vertical distribution of methane-oxidizing bacteria (methanotrophs) in the sediments of the Xianghai wetland, Songnen Plain, northeast China

Purpose

Methanotrophs in wetlands are of great importance because up to 90 % of the methane (CH₄) produced in such wetlands could be oxidized by methanotrophs before reaching the atmosphere. The Xianghai wetland of Songnen Plain represents an important ecosystem in northeast China. However, methanotrophic characteristics in this ecosystem have not been studied in detail. The aim of this study is to give an overview of methanotrophic diversity and vertical distribution in the sediments of this important wetland.

Materials and methods

Sediment cores were collected from three freshwater marshes, each dominated by a particular vegetation type: Carex alata, Phragmites australis and Typha orientalis. The diversity of methanotrophs was studied by phylogenetic analysis of both the 16S rRNA gene and the particulate methane monooxygenase (pmoA) gene. Methanotroph abundance was determined by quantitative PCR (qPCR) targeting the pmoA gene; group-specific pmoA gene quantification was also used to estimate the abundance of each methanotrophic group.

Results and discussion

16S rRNA and pmoA gene homological analysis revealed the presence of type Ia, Ib and II methanotrophs. Novel pmoA sequences distantly affiliated to cultured Methylococcus sp. were detected, implying the existence of novel methanotrophs in the wetland. Most obtained representatives of Methylobacter genus (both 16S rRNA and pmoA genes) were closely clustered in relation to sequences acquired from the Zoige wetland, Tibet and Siberia permafrost soils, therefore suggesting methanotrophs belonging to Methylobacter genus shared characteristics with methanotrophs in cold areas. The dominance of type I methanotrophs (especially the Methylobacter genus) was detected by both clone library analysis and group-specific qPCR assay. The relatively high methanotroph diversity and pmoA copy numbers measured in the T. orientalis marsh sediments indicated that vegetation type played an important role during CH₄ oxidation in the wetland.

Conclusions

We present the first data set on methanotroph diversity and vertical distribution in the sediments of the Xianghai wetland. DNA sequences information of Methylococcus-like methanotrophs in the wetland will facilitate the isolating of novel methanotrophs from the wetland. In a worldwide context, our study has enriched the database of genotypic diversity of methanotrophs, which will help in the understanding of the geographical distribution of methanotrophic communities.     

Factors influencing variability of proteolytic genes and activities in arable soils

Microorganisms, capable of proteolysis, are widely distributed in soil but almost nothing is known about the abundance of genes related to protein degradation and the regulation of their activity in terrestrial ecosystems. Therefore, the aim of this study was: (1) to quantify two bacterial genes involved in protein degradation, (2) to investigate factors affecting the abundance of these genes, and (3) to relate this data to potential proteolytic activities. For this purpose, an arable field in southern Germany under integrated management was studied. The uniformly managed field showed pronounced soil heterogeneity with four different soil types. In April, July and October 2003, soil samples were taken from the four soil types at three different depths. We applied a real-time PCR assay for quantification of subtilisin (sub) and neutral metalloprotease (npr) genes, both encoding for extracellular proteases, as well as the 16S rRNA gene representing a rough estimate of the size of the bacterial populations. Potential proteolytic activity was measured using casein as a substrate. Both soil type and time of sampling influenced the size and activity of the bacterial protease genes under investigation. Total nitrogen and carbon availability was, beside soil texture, the main factor responsible for the observed changes in the abundance of proteolytic genes and potential proteolytic activity. Whereas a positive relationship was found between sub and npr gene copy numbers and the number of 16S rRNA gene copies in all cases, a positive relationship between sub and npr coding genes and potential proteolytic activity was only found for sandy soils. This indicates that sandy soils cannot stabilize proteolytic enzymes and the activity of npr and sub genes is strictly dependent on the presence of the corresponding genes. In contrast, in clay soils proteolytic activity was not correlated with the abundance of the genes analyzed, probably due to the stabilization of the proteolytic enzymes.     

Biochar soil amendment increased bacterial but decreased fungal gene abundance with shifts in community structure in a slightly acid rice paddy from Southwest China

Biochar’s role on greenhouse gas emission and plant growth has been well addressed. However, there have been few studies on changes in soil microbial community and activities with biochar soil amendment (BSA) in croplands. In a field experiment, biochar was amended at rates of 0, 20 and 40 t ha⁻¹ (C0, C1 and C2, respectively) in May 2010 before rice transplantation in a rice paddy from Sichuan, China. Topsoil (0–15 cm) was collected from the rice paddy while rice harvest in late October 2011. Soil physico-chemical properties and microbial biomass carbon (MBC) and nitrogen (MBN) as well as selected soil enzyme activities were determined. Based on 16S rRNA and 18S rRNA gene, bacterial and fungal community structure and abundance were characterized using terminal-restriction fragment length polymorphism (T-RFLP) combined with clone library analysis, denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR assay (qPCR). Contents of SOC and total N and soil pH were increased but bulk density decreased significantly. While no changes in MBC and MBN, gene copy numbers of bacterial 16S rRNA was shown significantly increased by 28% and 64% and that of fungal 18S rRNA significantly decreased by 35% and 46% under BSA at 20 and 40 t ha⁻¹ respectively over control. Moreover, there was a significant decrease by 70% in abundance of Methylophilaceae and of Hydrogenophilaceae with an increase by 45% in Anaerolineae abundance under BSA at 40 t ha⁻¹ over control. Whereas, using sequencing DGGE bands of fungal 18S rRNA gene, some bands affiliated with Ascomycota and Glomeromycota were shown inhibited by BSA at rate of 40 t ha⁻¹. Significant increases in activities of dehydrogenase, alkaline phosphatases while decreased β-glucosidase were also observed under BSA. The results here indicated a shift toward a bacterial dominated microbial community in the rice paddy with BSA.     

Effects of super absorbent polymers on soil microbial properties and Chinese cabbage (Brassica chinensis) growth

Purpose

New water retention materials, super absorbent polymers (SAPs), have shown the potential to improve some soil physicochemical properties and promote growth of some crop species in arid and semi-arid areas. However, the impacts of SAPs on soil microbial properties are unclear. This study was conducted to clarify the effects of two SAPs on soil microbial properties and Chinese cabbage (Brassica chinensis) growth under different water conditions in the greenhouse.

Materials and methods

Experimental conditions included different irrigation conditions and different quantities of SAPs. Chinese cabbage was harvested after 1-month growth in the greenhouse. Meanwhile, soil samples were collected and sieved (<2-mm mesh). Some of the soils were kept at ?4 °C for analysis of soil physicochemical properties, and some at ?20 °C for analysis of soil microbial properties. Chinese cabbage samples were thoroughly washed with deionized water for the measurement of fresh weight, shoot length, and root length.

Results and discussion

The effects from SAPs were not obvious under water sufficient (WC1, watered every 2 days, and WC2, watered every 4 days) since plant properties were smaller in some SAP treatments than those in control. However, under water deficit (WC3, watered every 8 days), there were significant differences in plant shoot length and fresh weight between SAP treatments. There were also significant differences in relative soil water content between water condition (WC) or SAP treatments. The SAPs were beneficial for the formation of large aggregates. Under WC3, the soil organic matter (SOM) increased by 16.9 and 11.5 %, soil microbial biomass C (SMBC) by 32.5 and 19.3 %, and soil microbial respiration (SMR) by 52.1 and 37.2 % with Jaguar C (JC) and Jaguar S (JS), respectively. Under WC1 and WC2, significantly higher copy numbers of AOA in bulk treatment of JC were found compared with control treatment in this study. Under water deficit, the abundance of bacteria was significantly increased by application of SAPs. For almost every property of soil and plant, JC was showing better effects than JS.

Conclusions

Our results showed that cabbage growth was restricted under water-deficit conditions and the application of SAPs could conserve soil water and be useful for increasing cabbage growth under water deficit, improving SOM, SMBC, and SMR under different WC, and stimulating amoA gene AOA copy numbers and bacterial gene copy numbers. Thus, there should be no adverse effects of SAP application on soil microbial environment and Chinese cabbage growth.     

cry1Ac/cpti转基因大米水稻土中微生物群落的多样性研究

Two types of cry1Ac/cpti transgenic rice(GM1 and GM2)and their parental non-cry1Ac/cpti rice(CK1 and CK2)were planted in the field at Wufeng,Fujian Province,China for four years to investigate the influence of genetically modified rice on diversity of bacterial and fungal community in the paddy soil.The community composition and abundance of bacteria or fungi in the paddy soil were assessed at different growth stages of rice by denaturing gradient gel electrophoresis and real-time polymerase chain reaction based on 16S rRNA gene or SSU rRNA gene in the 4th year after the experimental establishment.The composition of bacterial or fungal community changed during rice growth,while no significant differences were observed between the fields cultivated with GM1and CK1,or between the fields cultivated with GM2 and CK2 in either bacterial or fungal community composition.The copy numbers of bacterial 16S rRNA gene in the soils with CK1,CK2,GM1 and GM2 ranged from 5.64×1011to 6.89×1011copies g-1dry soil at rice growth stages,and those of fungal SSU rRNA gene from 5.24×108to 8.68×108copies g-1dry soil.There were no marked differences in the copies of bacterial 16S rRNA gene or fungal SSU rRNA gene between CK1 and GM1 or between CK2 and GM2at any growth stage of rice.Planting cry1Ac/cpti transgenic rice had no significant effect on composition and abundance of bacterial and fungal community in paddy soil during the rice growing season at least in the short term.     

Potential for the alleviation of arsenic toxicity in paddy rice using amorphous iron-(hydr)oxide amendments

A pot culture experiment was conducted to investigate the effects of amorphous iron-(hydr)oxide (Am-FeOH) amendments on arsenic (As) availability and its uptake by rice ( Oryza sativa L. cv. BR28) irrigated with As-contaminated water. A rhizobag system was established using 3.5 L plastic pots, each containing one central compartment for plant growth, a middle compartment and an outside compartment. Three levels of laboratory-synthesized Am-FeOH (0, 0.1 and 0.5% w/w) were used to amend samples of the As-free sandy loam paddy soil placed into each compartment of the rhizobag system. The soils were submerged with a solution containing 5 mg L⁻¹ As(V). Two-week-old rice seedlings were planted in the central compartments and cultured for 9 weeks under greenhouse conditions. The addition of 0.1% Am-FeOH to the soil irrigated with As-contaminated water improved plant growth, reduced the As concentration in the plants and enhanced Fe-plaque formation on the root surfaces. Analysis of soil solution samples collected during the experiment revealed higher pH levels and lower redox potentials in the soils amended with Am-FeOH at the onset of soil submergence, but later the soil solution collected from the 0.1% Am-FeOH treatment was slightly acidic and more oxidized than the solution from the 0% treatment. This indicated active functioning of the roots in the soil treated with 0.1% Am-FeOH. The concentrations of As(III) in the soil solution collected from the central compartment were significantly reduced by the Am-FeOH amendments, whereas in the soil treated with 0% Fe, As(III) accumulated in the rhizosphere, particularly during the late-cultivation period. The improvement in plant growth and reduction in As uptake by plants growing in the Am-FeOH treated soil could be attributed to the reduction of available As in the soil solution, mainly as a result of the binding of As to the Fe-plaque on the root surfaces.     

Response of soil microbial diversity to land-use conversion of natural forests to plantations in a subtropical mountainous area of southern China

Land-use conversion can affect the soil microbial community diversity, soil organic matter and nutrient cycling. In this study, soils within a representative land-use sequence were sampled in a subtropical region of China, including four natural forests, Altingia gracilipes Hemsl. (ALG), Cinnamomum chekiangense Nakai (CIC), Castanopsis fargesii Franch. (CAF), and Tsoongiodendron odorum Chun (TSO), and two plantations, Cunninghamia lanceolata (Lamb.) Hook. (CUL) and a citrus orchard (Citrus reticulata Blanco). The soil microbial diversity was investigated by phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE) and real-time quantitative polymerase chain reaction (PCR). Results showed that microbial community diversity exhibited distinct patterns among land-use types. After conversion of natural forests to plantations, the amount of PLFA and the number of bacterial 16?S rRNA gene copies were reduced significantly, as well as the number of DGGE bands. The average quantity of PLFA was lower by 31% in the CUL plantation and 57% in the citrus orchard, respectively, than in natural forests. Simultaneously, the average copy numbers of the bacterial 16?S rRNA gene were significantly decreased from 8.1?×?10^10?g^?1?dry weight (DW) in natural forest to 4.9?×?10^10?g^?1 DW in CUL plantation, and 3.1?×?10^10?g^?1 DW in the citrus orchard. Such negative responses of soil microbes to conversion of natural forests to plantations could mainly result from decreases in soil organic carbon and necessary elements for growth during land-use conversion, as revealed by statistical analysis. Our results suggested that the soil microbial diversity was indirectly in?uenced by land-use types in the mid-subtropical mountainous area of southern China. Changes in the amount of litterfall and the soil nutrient status that resulted from land-use conversion drove these indirect changes. Furthermore, deliberate management brought negative effects on soil microbes, which is not beneficial to the sustainability of the ecosystem.     

Burrowing activity of the earthworms Lumbricus terrestris and Aporrectodea giardi and consequences on C transfers in soil

Two earthworms species, Lumbricus terrestris (epianecic) and Aporrectodea giardi (anecic) were incubated in microcosms with an epigeic ¹³C-labelled litter for 246 d. At the end of the experiment, different soil compartments (surface casts, walls and peripheries of burrows, and surrounding soil) were sampled for ¹³C analysis. Two-dimensional images acquired using X-ray computed tomography allowed to estimate the weight of the ‘burrow wall’ and ‘burrow periphery’ compartments which are required to establish C balance. In the case of L. terrestris, the formed structures were more C litter enriched compared to the other species. The permanent character of the burrow system could lead to a high and constant enrichment of the entire burrow system. As consequence, the percentage of C litter in the ‘burrow wall’ and ‘burrow periphery’ compartments was important in spite of their low volume. The denser system developed by A. giardi resulted in C litter dilution in the whole formed structures. The C litter enrichment decreased with the soil depth, but owing to the intensity of the burrowing activity, the C litter transfers into the ‘burrow walls’ and ‘burrow periphery’ were important and the C litter was homogeneously distributed throughout the whole column.     

Biosurfactant in Membrane Separation of Atrazine from Water

This study examines the effects of land use change on nitrate concentration and the abundances of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and narG-containing denitrifiers in shallow groundwater. The results reveal a general increase of nitrate in shallow groundwater following the change of land use from paddy fields to vegetable patches. Furthermore, a significant relationship between NO₃ ^?-N concentrations was observed both in groundwater and in soil at soil depths of 0–20, 20–40, 40–60, 60–80, and 80–100 cm. With regard to gene abundance in groundwater, the AOB amoA gene was most abundant and the AOA amoA gene copy numbers were lowest from the field with long-term paddy cultivation compared with the field under vegetable cultivation. The narG gene copy numbers were higher from the field under short-term vegetable cultivation compared with fields under long-term vegetable cultivation. The NO₃ ^?-N concentrations in groundwater correlated positively with AOA amoA gene copy numbers, negatively with the AOB amoA gene, but with no significant relationship with the narG gene. In conclusion, land use change from paddy fields to vegetable patches increases nitrate in groundwater, which is correlated significantly with nitrate in soil and the abundance of the amoA gene, but is not related to the narG gene in groundwater. This study also suggests that the removal of groundwater nitrate pollution is not feasible through biological denitrification without additional denitrifiers and that it might even become more aggravated because of the AOA.     

Molecular and physiological characterisation of psychrotrophic hydrocarbon-degrading bacteria isolated from Terra Nova Bay (Antarctica)

A set of 21 Antarctic marine bacteria isolated from the Ross Sea and able to utilise diesel fuel as the sole carbon and energy source was characterised. Isolates were analysed by amplified 16S rDNA restriction analysis using the enzyme AluI, resulting in two different groups corresponding to different bacterial species. These species were assigned to the genera Rhodococcus and Alcaligenes, on the basis of 16S rDNA sequencing. This low degree of inter-specific biodiversity was parallel to a low intra-specific biodiversity, as shown by Random Amplified Polymorphic DNA analysis. Then, a 550-bp DNA fragment coding for the inner region of alkane mono-oxygenase was PCR-amplified from the genome of each strain. The phylogenetic analysis of the sequence of the putative AlkB protein coded for by the amplified DNA fragment revealed that these alkB genes were very likely inherited by horizontal gene transfer. Lastly, the analysis of the biodegradation ability of four strains revealed two different strategies of hydrocarbon uptake, mediated either by bio-surfactants and peculiar of Rhodococcus isolates, or by membrane modifications and shown by Alcaligenes isolates. In order to understand the interrelationships between hydrocarbon-degrading isolates, the dynamics of two strains, belonging to Rhodococcus and Alcaligenes, grown together in a co-culture was also followed over a seventeen days period.     

Microfungal communities in soil,litter and casts of Lumbricus terrestris L. (Lumbricidae): a laboratory experiment

The anecic earthworm Lumbricus terrestris L. was kept in laboratory microcosms containing beech forest soil without litter, with beech leaf litter or with lime leaf litter. The structure of microfungal communities in soil, litter and fresh and aged (100 days) earthworm faeces was analysed using the washing and plating technique. The passage of mineral soil through the gut of L. terrestris affected the structure of the fungal community only little. In contrast, in the litter treatments the structure of the fungal community in fresh earthworm casts significantly differed from that in soil and litter. The majority of soil and litter inhabiting fungi survived passage through the gut of L. terrestris and the fungal community in casts consisted of a mixture of soil and litter inhabiting fungi. However, the frequency of Cladosporium spp., Alternaria spp., Absidia spp., and other taxa was strongly reduced in fresh casts. The degree of colonization of litter particles (number of isolates per number of plated particles) also decreased, but some fungi (mainly Trichoderma spp.) benefited from gut passage and flourished in fresh casts. During ageing of cast material the dominance structure of the fungal community changed. Both the degree of colonization of organic particles and the species diversity increased and approached that in soil. However, the structure of the fungal community in casts remained cast specific even after 100 days of incubation. It is concluded that the feeding and burrowing activity of L. terrestris accelerates the colonization of litter by the edaphic mycoflora but also extends the range of occurrence of litter-associated fungi into mineral soil layers.