Biodegradation of recalcitrant compounds and phthalates by culturable bacteria isolated from Liometopum apiculatum microbiota.

The predicted changes in precipitation patterns because of global change have profound effects on terrestrial ecosystems. In the present study, the principle and design details of a rainfall enrichment system (RAINES) for open field experiments in semi-arid and arid ecosystems are shown. The rainfall intensity, validity and uniformity of this experimental facility were also tested. During the period from 2008 to 2010, our data showed that the RAINES was able to simulate rainfall events with different rainfall sizes, frequencies and timing. The greatest advantage of the RAINES was its high uniformity in rainfall distribution over a relatively large experimental surface area (>90 m2), which was important for experimental studies of semi-arid and arid ecosystems where vegetation distribution is sparse. The rainfall validity of RAINES was steadily at 66% or higher as long as the hydraulic pressure exceeded 1.4 KPa and the wind speed was below 2.5 m s-1. Since the RAINES is light-weight, inexpensive and versatile enough to be used to simulate various rainfall events with needed properties in remote fields, it is able to provide reliable simulated rainfall in the field for studying possible responses of soil and vegetation processes to rainfall change in arid and semi-arid ecosystems. The application of the RAINES will improve our understanding on the relationship between water availability and ecosystem processes in arid and semi-arid ecosystems, which will provide useful knowledge for the protection, restoration and sustainable management of semi-arid and arid desert ecosystems world.

Abstract. Since seeds are the principle means by which plants move across the landscape, the final fate of seeds plays a fundamental role in the assemblage, functioning and dynamics of plant communities. Once seeds land on the soil surface after being dispersed from the parent plant, they can be moved horizontally by surface runoff. In arid and semiarid patchy ecosystems, where seeds are scattered into a very heterogeneous environment and intense rainfalls occur, the transport of seeds by runoff to new sites may be an opportunity for seeds to reach more favourable sites for seed germination and seedling survival. Although seed transport by runoff may be of vital importance for the recruitment of plants in these ecosystems, it has received little attention in the scientific literature, especially among soil scientists. The main goals of this review paper are (1) to offer an updated conceptual model of seed fate with a focus on seed destiny in and on the soil; (2) to review studies on seed fate in overland flow and the ecological implications seed transport by runoff has for the origin, spatial patterning and maintenance of patches in arid and semiarid patchy ecosystems; and finally (3) to point out directions for future research. This review shows that seed fate in overland flow may result either in the export of seeds from the system (seed loss) or in the spatial redistribution of seeds within the system through short-distance seed movements (seed displacement). Seed transport by runoff depends on rainfall, slope and soil characteristics. Susceptibility of seed removal varies highly between species and is mainly related to seed traits, including seed size, seed shape, presence of appendages, and ability of a seed to secrete mucilage. Although initially considered as a risk of seed loss, seed removal by runoff has recently been described as an ecological driver that shapes plant composition from the first phases of the plant life by favouring species with seeds able to resist erosion and by selecting for plant traits that prevent seed loss. Moreover, the interaction of seed transport by overland flow with the high seed trapping capacity of vegetated patches results in a "patch-to-patch" transport of seeds that plays a relevant role in vegetation establishment and patterning in arid and semiarid patchy ecosystems. Overall, this review shows how the knowledge about seed fate in overland flow can be used to explain a number of important characteristics of whole plant communities. It also underlines important gaps in knowledge that should be filled in. Future lines of research are proposed in order to broaden our understanding of the origin, maintenance and dynamics of patchiness in arid and semiarid ecosystems and to improve restoration success of intensively eroded ecosystems. Among the most exciting challenges, empirical studies are needed to understand the relevance of short-distance seed displacements in the origin and maintenance of patchiness, addressing the feedbacks between structure and function and abiotic and biotic components, in order to validate existing models about the dynamics of arid and semiarid ecosystems and help to predict future changes under the scenarios of climate change.

Shrubs are widely distributed in semi-arid and arid ecosystems. Understanding shrub effects on alpha and beta diversity of soil fauna in arid and semiarid ecosystems could lead to promotion of biodiversity conservation and sustainable management. Yet the extent to which shrubs can influence beta diversity of soil fauna and different body size in arid and semiarid ecosystems is unknown. An investigation of soil fauna, macrofauna, and mesofauna beneath shrub canopy and in open spaces was conducted in the Donddashan Nature Reserve (a semiarid grassland ecosystem in China). Shrubs significantly increased the alpha diversity (richness and Shannon index), but significantly decreased the beta diversity and the nestedness component. Moreover, shrub effects differed among soil fauna of different body size. Shrubs significantly increased the abundance and Shannon index of mesofauna, whereas there were no significant effects on macrofauna between shrubs and open spaces. Shrubs significantly decreased the beta diversity of mesofauna, but significantly increased beta diversity and the turnover component of macrofauna. Piecewise structural equation modelling (SEM) showed that shrubs had an indirect effect on soil fauna diversity through mesofauna diversity. Results highlighted the crucial role that shrubs have in maintaining alpha diversity of soil fauna in arid ecosystem, and also demonstrated the divergent shrub effects on beta diversity of soil fauna, mesofauna, and macrofauna. This suggests a need to examine different taxonomic groups to gain a better understanding of ecological consequences of shrubs.

Background Future climate projections indicate shifts in intra-annual precipitation patterns, with intensified rainfall events and prolonged dry periods. These changes may alter soil biotic communities and their interactions within food webs, particularly in semi-arid and arid ecosystems. However, the extent to which varying rainfall regimes and semi-arid and arid conditions influence multitrophic associations remains poorly understood. Methods We leveraged a four-year rainfall manipulation experiment across six dryland sites in eastern Australia, representing arid and semi-arid ecosystems with varying, high and low levels of rainfall variability (CV) making three different climatic conditions. Rainfall treatments simulated increased (+ 65%) and reduced (-65%) precipitation relative to ambient conditions. We studied multitrophic co-occurrence network among bacteria, fungi, protists, and nematodes, representing key components of the soil food web, and assess their associated changes to varying rainfall and climatic conditions. Results Climatic differences between arid and semi-arid ecosystems were the primary drivers of soil biotic community composition, whereas rainfall treatments had minimal influence. Multitrophic co-occurrence networks varied significantly across climatic conditions, with increasing aridity promoting more positive associations among bacterial nodes. Bacteria, fungi, and their interactions were central to the belowground multitrophic network structure. In particular, stress-tolerant oligotrophic bacteria and pathotrophic fungi played key roles, with mean annual precipitation (MAP) identified as a critical determinant. Conclusions Our findings suggest that aridity-driven shifts in biotic interactions may restructure belowground food webs in dryland ecosystems. The increasing dominance of oligotrophic bacteria and fungal pathotrophs under arid conditions highlights potential consequences for soil functioning and plant-soil interactions in response to changing precipitation regimes.

The enzymatic activities of bacteria isolated from the digestive tracts of caterpillars and the pupal contents of Automeris zugana and Rothschildia lebeau was studied. This digestive tract represents an extreme microenvironment due to its high pH and presence of antimicrobial substances secreted by the insect or derived from ingested plant tissue. At the same time, it contains large amounts of nutrient-rich food, for which microbes may compete among themselves and with the caterpillar. There is little information about the microbiota associated with tropical caterpillar guts, although bacteria from different genera have been isolated from gut and pupae samples. The study of the enzymatic activities generated by these organisms constitutes a starting point to understand their metabolic and physiological relationships with their hosts, and to find enzymes that have potential biotechnological applications. In this study we evaluated several enzymatic activities in two collections of bacteria isolated from caterpillar guts and pupae of the tropical lepidopteran species A. zugana and R. lebeau. Bacteria grown under aerobic conditions were tested for an array of enzymes, including gelatinases, caseinases, lipases, esterases, cellulases, xylanases, amylases and chitinases. Both collections displayed similar patterns of enzymatic activity. No isolate showed activity for all enzymatic tests, but as a whole, at least some bacteria in each collection were able to degrade each substrate tested. Isolates with the same taxonomic identification obtained from caterpillar guts and pupae had almost the same enzymatic activities. In both collections, it was possible to group bacterial isolates according to their enzyme activity pattern. In addition to a heterogeneous ensemble of isolates exhibiting two or less enzymatic activities, there were two groups with at least five activities that showed an apparent specialization for the substrates they were able to use. The first consisted exclusively of isolates of the family Enterobacteriaceae, which were positive for lipolytic and chitinolytic activities, but completely lacked amylasic, cellulolytic and xylanolytic activities. The second group, composed mainly of Gram-positive rods, exhibited the opposite pattern: they were positive for amylasic, cellulolytic and xylanolytic activities, lacked chitinolytic activity and had few isolates with lipolytic activity. This work forms the foundation for future research to explore the biotechnological potential of bacterial isolates from caterpillar guts.

To sustainably operate a biorefinery with a low cost input in a commercial setting, the hydrolysis of lignocellulosic biomass must be undertaken in a manner which will impart environmental tolerance while reducing fermenter inhibitors from the delignification process. The challenge lies with the highly recalcitrant lignin structure, which limits the conversion of the holocelluloses to fermentable total reducing sugars (TRS). Due to these challenges, sustainable and innovative methods to pre-treat biomass must be developed for delignocellulolytic operations. Herein, Nepenthes mirabilis digestive fluids shown to have ligninolytic, cellulolytic and xylanolytic activities were used as an enzyme cocktail to hydrolyse mixed agro-waste constituted by Citrus sinensis (orange), Malus domestica (apple) peels, cobs from Zea mays (maize) and Quercus robur (oak) yard waste. The digestive fluids contained carboxylesterases (529.41 ± 30.50 U/L), β-glucosidases (251.94 ± 11.48 U/L) and xylanases (36.09 ± 18.04 U/L), constituting an enzymatic cocktail with significant potential for the reduction in total residual phenolic compounds (TRPCs), while being appropriate for holocellulose hydrolysis. Furthermore, the maximum TRS obtainable was 310 ± 5.19 mg/L within 168 h, while the TRPCs were reduced from 6.25 ± 0.18 to 4.26 ± 0.09 mg/L, which was lower than that observed when conventional methods were used. Overall, N. mirabilis digestive fluids demonstrated an ability to support biocatalytic processes with minimised cellulases hydrolysis interference. Therefore, the digestive enzymes in N. mirabilis pods can be used in an integrated system for feedstock hydrolysis in a second generation biorefinery.

Effect of repeated drying-rewetting cycles on soil extracellular enzyme activities and microbial community composition in arid and semi-arid ecosystems

The bacterial community of Daqu affects its characteristics and functions by their metabolic products, such as amylase, protease, esterase. In this study, barcoded pyrosequencing was used to analyse the bacterial communities of three kinds of Daqu for light-flavour Chinese liquor brewing. A total of 13672 sequences were identified as bacterial sequences. The Shannon index of QC, HX and GT for clusters sharing 97% homology was 5·0, 4·2 and 4·2, respectively, indicating that QC had the highest biodiversity. The Good's coverage index of QC, HX and GT was 88·2, 93·4 and 93%, respectively, indicating that the vast majority of phylotypes have been detected. Among the three kinds of Daqu, the majority of annotated reads were assigned to two phyla (Firmicutes and Actinobacteria). The phylum Firmicutes was the most abundant group in QC (74·2%), HX (81·4%) and GT (98·6%), and the phylum Actinobacteria was the second in QC (23·9%), HX (17·9%) and GT (1·1%). There were many lactic acid bacteria in all three kinds of Daqu QC (45·8%), HX (46·3%) and GT (24·7%). In addition, the most abundant family in GT was Bacillus, accounting for 65·0%, while in HX, the families Thermoactinomycetaceae and Streptomycetaceae accounted for 19·5 and 14·1%, respectively, and in QC, 13·1% were Streptomycetaceae, 12·2% were heterofermentative Leuconostocaceae. There are three kinds of Daqu (starter material) used for famous Chinese light-flavour liquor brewing, that is Qingcha, Hongxin and Houhuo. Since Daqu was fermented in an open environment, the microbiology communities were different with different kind of Daqu. Objective bacterial communities determined by barcoded pyrosequencing help to speculate possible metabolic productions, even to guess the function of many kind of Daqu in light-flavour liquor brewing.

Diversity analyses of microbial communities in petroleum samples from Brazilian oil fields

The aim of this study was to test the hypothesis that N2 fixation by free-living microorganisms is a quantitatively important process in arid and semiarid ecosystems and that N2 fixation per unit microbial biomass increases with increasing aridity. For this purpose, we studied soils along a precipitation gradient in Chile (ranging from 10 to 1084 mm mean annual precipitation), comprising the arid, semiarid, Mediterranean, and humid climate zone.We sampled three soil depth increments (0–10, 10–20, and 20–30 cm) at four sites along the precipitation gradient, and measured the rates of N2 fixation by free-living microorganisms (using 15N–N2) and microbial respiration at two soil water contents (30% and 65% soil water holding capacity (WHC)). In addition, we determined carbon (C) and nitrogen (N) contents in roots, microbial biomass (MB) and soil as well as the soil Δ14C and δ15N signature.We found that the soil total organic C (TOC) content and the total soil organic C-to-total N (TOC:TN) ratio increased with declining aridity from the arid to the humid site by a factor of 44 and 1.9, respectively. The rate of N2 fixation per unit microbial biomass (qN2) decreased with declining aridity from 51.0 ng N mg−1 MBC d−1 at the arid site to 2.3 ng N mg−1 MBC d−1 at the humid site, at 30% WHC. The ratio of respiration-to-N2 fixation increased very strongly with declining aridity along the precipitation gradient by a factor of about 1760 from the arid to the humid site. N2 fixation per m2 was higher at the humid site than at the arid site by a factor of two, while microbial respiration was 186 times higher at the humid than at the arid site. At 65% soil WHC, N2 fixation per m2 was highest at the Mediterranean site, which is in accordance with the low natural abundance soil δ15N at this site.In conclusion, the study shows that N2 fixation by free-living microorganisms is a quantitatively important process in (semi-)arid ecosystems and that qN2 is high in (semi-)arid ecosystems. The high N2 fixation rate relative to the soil TOC and the low C:N ratio of organic matter inputs to the soils are very likely the most important reasons why the soil TOC:TN ratio is typically low in arid and semiarid ecosystems.

This review examines the following questions: (1) do soil fauna play an important regulatory role in decomposition and mineralization processes in arid and semiarid ecosystems? (2) if important, what are the mechanisms of the rate regulation, and (3) what are the management implications of these relationships? Because termites process more than half of the surface litter in hot deserts, this review focuses on faunal effects on buried litter and roots. Elimination of soil arthropods reduced rates of mass loss and coupled mass loss to soil moisture. With arthropods present soil moisture accounted for less than 50% of the variation in mass loss. Other experiments demonstrated that regulation of mass loss results from predatory mites regulating the population density of grazers, thereby preventing overgrazing of the fungi and bacteria. The regulation of microbial grazers by soil microarthropods also affects rates of mineralization and nutrient immobilization. Populations of small fungus grazing mites...

According to the United Nations (UNEP, Agenda 21), approximately one sixth of the world’s population, 70% of all drylands with a total area of 3.6 billion hectares, and a quarter of the total land surface of the earth is endangered by desertification. The most obvious consequences are increasing poverty and the growing damage to 3.3 billion hectares of rangeland. These impressive figures illustrate the importance of developing mechanisms for combating desertification. However, there is an increasing number of scientists who doubt the accuracy of these figures and who speak of ‘the myth of desertification’ as a publicity tool (e.g., Thomas & Middleton 1994). Their criticism is based on the idea that dryland ecosystems might after all be well adapted to disturbances and may exhibit good recovery characteristics. Nevertheless, it has been increasingly recognized that arid and semiarid ecosystems often exhibit complex non-equilibrium dynamics involving complicated nonlinear processes and stochastic event-driven behavior (Westoby et al. 1989; Walker 1993). Vegetation changes generally occur unpredictably in the short term (years) in response to rainfall, and episodically in the long term (several decades) in response to rare events, or due to grazing pressure, climatic change, altered disturbance regimes, or a combination of these factors. The complex dynamics of arid and semiarid ecosystems and especially the mismatch between observation times (years) and time scales of vegetation change (centuries) make it difficult to fully understand their long-term dynamics (Wiegand et al. 1995; Jeltsch et al. 1996). Hence, it is extremely difficult to establish whether an area is undergoing progressive, long-term decline in biodiversity and productivity (desertification), or whether it is merely suffering shortterm drought, from which the land may recover if human impact is reduced or eliminated. But for developing management strategies for sustained animal production and species conservation, it is necessary to know how resilient arid and semiarid ecosystems really are, and to assess their potential to recover from serious natural or human disturbances or stress. Long-term ecological monitoring and interdisciplinary approaches to interaction between rainfall, geology and ecology are required in order to gain a better understanding of long-term dynamics in arid and semiarid systems. These approaches include both field studies and modelling studies. The latter can help to extrapolate local information and knowledge gathered on shorter time scales to larger spatial and temporal scales. This knowledge originating from field and modeling studies forms an indispensable basis for identifying key factors and processes that shape the potential for both desertification and recovery therefrom. In the following we briefly summarize and link various papers (all this issue) on field and modeling studies that are based on contributions to the INTECOL symposium ‘Long-term dynamics in arid and semi-arid ecosystems’ in Florence, 1998, or that were inspired through discussions during and after the symposium

The diversity of 184 isolates from rhizosphere and bulk soil samples taken from the Ni hyperaccumulator Alyssum murale, grown in a Ni-rich serpentine soil, was determined by 16S rRNA gene analysis. Restriction digestion of the 16S rRNA gene was used to identify 44 groups. Representatives of each of these groups were placed within the phyla Proteobacteria, Firmicutes and Actinobacteria by 16S rRNA gene sequence analysis. By combining the 16S rRNA gene restriction data with the gene sequence analysis it was concluded that 44.6% (82/184) of the isolates were placed within the phylum Proteobacteria, among these 35.9% (66/184) were placed within the class α-Proteobacteria, and 20.7% (38/184) had 16S rRNA gene sequences indicative of bacteria within genera that form symbioses with legumes (rhizobia). Of the remaining isolates, 44.6% (82/184) and 5.4% (10/184) were placed within the phyla Actinobacteria and Firmicutes, respectively. No placement was obtained for a small number (10/184) of the isolates. Bacteria of the phyla Proteobacteria and Actinobacteria were the most numerous within the rhizosphere of A. murale and represented 32.1% (59/184) and 42.9% (79/184) of all isolates, respectively. The approach of using 16S rRNA gene sequence analysis in this study has enabled a comprehensive characterization of bacteria that predominate in the rhizosphere of A. murale growing in Ni-contaminated soil.

Canada is currently implementing a site selection process to identify a location for a deep geological repository (DGR) for the long-term storage of Canada's used nuclear fuel, wherein used nuclear fuel bundles will be sealed inside copper-coated carbon steel containers, encased in highly compacted bentonite clay buffer boxes, and sealed deep underground in a stable geosphere. Because a DGR must remain functional for a million years, it is important to examine ancient natural systems that serve as analogues for planned DGR components. Specifically, studying the microbiology of natural analogue components of a DGR is important for developing an understanding of the types of microorganisms that may be able to grow and influence the long-term stability of a DGR. This study explored the abundance, viability, and composition of microorganisms in several ancient natural analogues using a combination of cultivation and cultivation-independent approaches. Samples were obtained from the Tsukinuno bentonite deposit (Japan) that formed ∼10 mya, the Opalinus Clay formation (Switzerland) that formed ∼174 mya, and Canadian shield crystalline rock from Northern Ontario that formed ∼2.7 bya. Analysis of 16S rRNA gene amplicons revealed that three of the ten Tsukinuno bentonite samples analyzed were dominated by putative aerobic heterotrophs and fermenting bacteria from the phylum Actinobacteria, whereas five of the Tsukinuno bentonite samples were dominated by sequences associated with putative acidophilic chemolithoautotrophs capable of sulfur reduction. The remaining Tsukinuno bentonite samples, the Northern Ontario rock samples, and the Opalinus Clay samples generated inconsistent replicate 16S rRNA gene profiles and were associated primarily with contaminant sequences, suggesting that the microbial profiles detected were not sample-specific but spurious. Culturable aerobic heterotroph abundances were relatively low for all Tsukinuno bentonite samples, culturable anaerobic heterotrophs were only detected in half of the Tsukinuno samples, and sulfate-reducing bacteria (SRB) were only detected in one Tsukinuno sample by cultivation. Culture-specific 16S rRNA gene profiles from Tsukinuno clay samples demonstrated the presence of phyla Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes among aerobic heterotroph cultures and additional bacteria from the phyla Actinobacteria and Firmicutes from anaerobic heterotroph plate incubations. Only one nucleic acid sequence detected from a culture was also associated with its corresponding clay sample profile, suggesting that nucleic acids from culturable bacteria were relatively rare within the clay samples. Sequencing of DNA extracted from the SRB culture revealed that the taxon present in the culture was affiliated with the genus Desulfosporosinus, which has been found in related bentonite clay analyses. Although the crystalline rock and Opalinus Clay samples were associated with inconsistent, likely spurious 16S rRNA gene profiles, we show evidence for viable and detectable microorganisms within several Tsukinuno natural analogue bentonite samples.

The Bacillaceae family members are considered to be a good source of microbial factories for biotechnological processes. In contrast to Bacillus and Geobacillus, Anoxybacillus, which would be thermophilic and spore-forming group of bacteria, is a relatively new genus firstly proposed in the year of 2000. The development of thermostable microbial enzymes, waste management and bioremediation processes would be a crucial parameter in the industrial sectors. There has been increasing interest in Anoxybacillus strains for biotechnological applications. Therefore, various Anoxybacillus strains isolated from different habitats have been explored and identified for biotechnological and industrial purposes such as enzyme production, bioremediation and biodegradation of toxic compounds. Certain strains have ability to produce exopolysaccharides possessing biological activities including antimicrobial, antioxidant and anticancer. This current review provides past and recent discoveries regarding Anoxybacillus strains and their potential biotechnological applications in enzyme industry, environmental processes and medicine.