Impacts on soil microbial characteristics and their restorability with different soil disinfestation approaches in intensively cropped greenhouse soils.

The different impacts, especially on soil physicochemical and microbial characteristics, among disinfestation methods based on different principles (including physical, chemical, and biological) have not been illustrated well. Here, we used steam sterilization, dazomet fumigation, and reductive soil disinfestation (RSD) methods representative of physical, chemical, and biological soil disinfestation, respectively, to disinfest seriously degraded greenhouse soils before watermelon cultivation in one season. Compared with the control, RSD significantly decreased the soil nitrate content by 85.9% and the electrical conductivity by 52.0% and increased the soil pH to 7.44. Although all three soil disinfestations significantly decreased the abundance of the pathogen Fusarium oxysporum by 83.0-99.2%, their impacts on soil microbial characteristics were variable. Briefly, steam sterilization significantly changed multiple bacterial and fungal properties. Dazomet fumigation impacted mainly fungal properties, such as abundance, diversity, and community structure, but RSD significantly decreased bacterial diversity and altered the bacterial community structure. Although the differences mentioned above got smaller after watermelon cultivation, the plant performances differed dramatically in different soils. The largest plant biomass, fruit ratio, and yield were found in the RSD-treated soil, whereas the lowest fruit ratio and yield were found in the steam-sterilized soil. The soil nitrate content, electrical conductivity, bacterial diversity and community structure, and some specific microbial agents, such as Aspergillus, Cladosporium, and Pseudomonas, were correlated with plant performance. RSD is a promising soil disinfestation strategy to support plant growth in intensively cultivated greenhouse soils with serious problems, such as acidification, salinization, and pathogen accumulation.

Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils.

The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado sensu stricto soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and amoA genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c Thaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher amoA diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.

Effect of light intensity on the characteristics of algal-bacterial granular sludge and the role of N-acyl-homoserine lactone in the granulation.

The effects of light intensity on the development of algal-bacterial granular sludge (ABGS) were investigated over a period of 12 weeks. The ABGS developed at low light intensity (142 ±â€¯10 µmol m-2·s-1) exhibited excellent settling ability (SVI30 of 30.9 mL/g), COD and TN removal efficiencies (97.6% and 60.4%, respectively). High light intensity (316 ±â€¯12 µmol m-2·s-1) accelerated granular biomass growth (5.3 g/L) and enhanced the TP removal efficiency (83.7%). Extracellular polymeric substance (EPS) analysis revealed that low light intensity induced more large weight distribution protein production (9-12 kDa and 50-150 kDa), predominantly tryptophan and aromatic proteins. Furthermore, N-acyl-homoserine lactones (AHLs) with a side chain ≤ C10 were commonly shared in the ABGS, and the ABGS developed at low light intensity had a higher C6- and 3OC8-HSL content, which effectively promoted the biofilm formation. The add-back studies showed that the AHLs facilitated the regulation of EPS synthesis. Statistical analysis indicated that the AHLs content had a close correlation with the EPS production, the 50th percentile of the particle size distribution and microbial community assembly, suggesting that AHLs-mediated quorum sensing have an important ecological role in EPS expression and algal-bacterial granulation. Overall, this study describes the ABGS development at different light intensities and the mechanisms of ABGS formation treating synthetic domestic wastewater.

Hypothesis: Muon Radiation Dose and Marine Megafaunal Extinction at the End-Pliocene Supernova.

Considerable data and analysis support the detection of one or more supernovae (SNe) at a distance of about 50 pc, ∼2.6 million years ago. This is possibly related to the extinction event around that time and is a member of a series of explosions that formed the Local Bubble in the interstellar medium. We build on previous work, and propagate the muon flux from SN-initiated cosmic rays from the surface to the depths of the ocean. We find that the radiation dose from the muons will exceed the total present surface dose from all sources at depths up to 1 km and will persist for at least the lifetime of marine megafauna. It is reasonable to hypothesize that this increase in radiation load may have contributed to a newly documented marine megafaunal extinction at that time.

How ecological communities respond to artificial light at night.

Many ecosystems worldwide are exposed to artificial light at night (ALAN), from streetlights and other sources, and a wide range of organisms has been shown to respond to this anthropogenic pressure. This raises concerns about the consequences for major ecosystem functions and their stability. However, there is limited understanding of how whole ecological communities respond to ALAN, and this cannot be gained simply by making predictions from observed single species physiological, behavioral, or ecological responses. Research needs to include an important building block of ecological communities, namely the interactions between species that drive ecological and evolutionary processes in ecosystems. Here, we summarize current knowledge about community responses to ALAN and illustrate different pathways and their impact on ecosystem functioning and stability. We discuss that documentation of the impact of ALAN on species interaction networks and trait distributions provides useful tools to link changes in community structure to ecosystem functions. Finally, we suggest several approaches to advance research that will link the diverse impact of ALAN to changes in ecosystems.

ICRP Publication 136: Dose Coefficients for Non-human Biota Environmentally Exposed to Radiation.

Abstract ­: The diversity of non-human biota is a specific challenge when developing and applying dosimetric models for assessing exposures of flora and fauna from radioactive sources in the environment. Dosimetric models, adopted in Publication 108, provide dose coefficients (DCs) for a group of reference entities [Reference Animals and Plants (RAPs)]. The DCs can be used to evaluate doses and dose rates, and to compare the latter with derived consideration reference levels (DCRLs), which are bands of dose rate where some sort of detrimental effect in a particular RAP may be expected to occur following chronic, long-term radiation exposure, as outlined in Publication 124. These dosimetric models pragmatically assume simple body shapes with uniform composition and density, homogeneous internal contamination, limited sets of idealised sources of external exposure to ionising radiation for aquatic and terrestrial animals and plants, and truncated radioactive decay chains. This pragmatic methodology is further developed and systematically extended in this publication, which supersedes the DC values of Publication 108. Significant methodological changes since Publication 108 include: implementation of a new approach for external exposure of terrestrial animals with an extended set of environmental radioactive sources in soil and in air; considering an extended range of organisms and locations in contaminated terrain; transition to the contemporary radionuclide database of Publication 107; assessment-specific consideration of the contribution of radioactive progeny to DCs of parent radionuclides; and use of generalised allometric relationships in the estimation of biokinetic or metabolic parameter values. These methodological developments result in changes to previously published tables of DCs for RAPs, and revised values are provided in this publication. This publication is complemented by a new software tool, called 'BiotaDC', which enables the calculation of DCs for internal and external exposures of organisms with user-defined masses, shapes, and locations in the environment and for all radionuclides in Publication 107.

Low doses and non-targeted effects in environmental radiation protection; where are we now and where should we go?

The field of low dose radiobiology has advanced considerably in the last 30 years from small indications in the 1980's that all was not simple, to a paradigm shift which occurred during the 1990's, which severely dented the dose-driven models and DNA centric theories which had dominated until then. However while the science has evolved, the application of that science in environmental health protection has not. A reason for this appears to be the uncertainties regarding the shape of the low dose response curve, which lead regulators to adopt a precautionary approach to radiation protection. Radiation protection models assume a linear relationship between dose (i.e. energy deposition) and effect (in this case probability of an adverse DNA interaction leading to a mutation). This model does not consider non-targeted effects (NTE) such as bystander effects or delayed effects, which occur in progeny cells or offspring not directly receiving energy deposition from the dose. There is huge controversy concerning the role of NTE with some saying they reflect "biology" and that repair and homeostatic mechanisms sort out the apparent damage while others consider them to be a class of damage which increases the size of the target. One thing which has recently become apparent is that NTE may be very critical for modelling long-term effects at the level of the population rather than the individual. The issue is that NTE resulting from an acute high dose such as occurred after the A-bomb or Chernobyl occur in parallel with chronic effects induced by the continuing residual effects due to radiation dose decay. This means that if ambient radiation doses are measured for example 25 years after the Chernobyl accident, they only represent a portion of the dose effect because the contribution of NTE is not included.

Calculating the radiological parameters used in non-human biota dose assessment tools using ERICA Tool and site-specific data.

The substantial complexity in ecosystem-radionuclide interactions is difficult to be represented in terms of radiological doses. Thus, radiological dose assessment tools use typical exposure situations for generalized organisms and ecosystems. In the present study, site-specific data and radioactivity measurements of terrestrial organisms (grass and herbivore mammals) and abiotic components (soil) are provided. The retrieved data are used in combination with the ERICA Assessment Tool for calculation of radiological parameters. The process of radionuclide transfer within ecosystem components is represented using concentration ratios (CRs), while for the calculation of dose rates the dose conversion coefficient (DCC) methodology is applied. Comparative assessments are performed between the generic and assessment-specific radiological parameters and between the resulting dose rates. Significant differences were observed between CRs calculated in this study and those reported in the literature for cesium and thorium, which can easily be explained. On the other hand, CRs calculated for radium are in very good agreement with those reported in the literature. The DCCs exhibited some small differences between the reference and the assessment-specific organism due to mass differences. The differences were observed for internal and external dose rates, but they were less pronounced for total dose rates which are typically used in the assessment of radiological impact. The results of the current work can serve as a basis for further studies of the radiological parameters in environments that have not been studied yet.

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities.

The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.

The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont.

A new method of estimation of dose conversion coefficients for aquatic biota.

In order to develop the basis of an approach, through which we can comprehend the relationships of radiation exposures and dose, and dose and radiological effects, large numbers of dosimetric data are required. It is complex to estimate the dosimetry involved due to enormous variability of organism shapes, masses, and their natural habitats. This paper aims to develop an empirical equation, which correlates dose conversion coefficients (DCCs) with organism volume V, density ρ, source energy E and curve fitting coefficients. Compared with the values calculated by a Monte Carlo method, the mean relative deviation of the empirical-fitted DCCs are reasonably low for gamma external exposure and beta internal exposure. The empirical-fitted values are very close to those calculated using a simplified anatomical phantom, the ERICA Tool or a voxel phantom.

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

[Effect of X-ray micro-computed tomography on the metabolic activity and diversity of soil microbial communities in two Chinese soils].

OBJECTIVE: X-ray micro-computed tomography (micro-CT) technology, as used in the in situ and nondestructive analysis of soil physical structure, provides the opportunity of associating soil physical and biological assays. Due to the high heterogeneity of the soil matrix, X-ray micro-CT scanning and soil microbial assays should be conducted on the same soil sample. This raises the question whether X-ray micro-CT influences microbial function and diversity of the sample soil to be analyzed. METHODS: To address this question, we used plate counting, microcalorimetry and pyrosequencing approaches to evaluate the effect of X-ray--at doses typically used in micro-CT--on soil microorganisms in a typical soil of North China Plain, Fluvo-aquic soil and in a typical soil of subtropical China, Ultisol soil, respectively. RESULTS: In both soils radiation decreased the number of viable soil bacteria and disturbed their thermogenic profiles. At DNA level, pyrosequencing revealed that alpha diversities of two soils biota were influenced in opposite ways, while beta diversity was not affected although the relative abundances of some guilds were changed. CONCLUSION: These findings indicate that the metabolically active aspects of soil biota are not compatible with X-ray micro-CT; while the beta molecular diversity based on pyrosequencing could be compatible.

Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters.

UNLABELLED: There is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013 to August 2014) were used to identify microbes in seawater in four size fractions: >63 µm (zooplankton and large particles), 63 to 5 µm (particles), 5 to 1 µm (small particles/dividing cells), and <1 µm (free-living prokaryotes). Analyses of microbial community composition highlight the importance of the microhabitat (e.g., particle-associated versus free-living lifestyle) as communities cluster by size fraction, and the microhabitat explains more of the community variability than measured environmental parameters, including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1-µm and 5- to 1-µm fractions, none of the measured bulk seawater environmental variables are statistically significant in the larger-particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e., >63 µm), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria. IMPORTANCE: By comparing levels of particle-associated and free-living bacterial diversity at a coastal location over the course of 14 months, we show that bacteria associated with particles are generally more diverse and appear to be less responsive to commonly measured environmental variables than free-living bacteria. These diverse and highly variable particle-associated communities are likely driven by differences in particle substrates both within the water column at a single time point and due to seasonal changes over the course of the year.

Temperature-Dependent Expression of NodC and Community Structure of Soybean-Nodulating Bradyrhizobia.

In order to assess the physiological responses of bradyrhizobia and competition for the nodulation of soybean at different temperatures, we investigated the expression of the nodC gene at 20, 25, and 30°C and the abilities of bacteria to nodulate soybean in microcosms at day/night cultivation temperatures of 23/18°C, 28/23°C, and 33/28°C for 16/8 h. We tested five Bradyrhizobium USDA strains: B. diazoefficiens USDA 110(T) and 122, B. japonicum USDA 123, and B. elkanii USDA 31 and 76(T). The expression of nodC was up-regulated by increasing culture temperatures in USDA 110(T), 122, 31, and 76(T), but was down-regulated in USDA 123. The proportions of USDA 110(T) and 122 within the community were the greatest at 28/23°C. The population of USDA 31 increased, whereas that of USDA 123 decreased with increasing cultivation temperatures. On the other hand, infection by USDA 76(T) was not detected, and low numbers of USDA 76(T) nodules confirmed its poor nodulation ability. These results indicate that the competitiveness of and infection by USDA 110(T), 122, 123, and 31 for soybean nodulation depend on cultivation temperatures, and suggest that the temperature dependence of nodC expression affects the bradyrhizobial community structure.

Characterization of biofilm formation in natural water subjected to low-frequency electromagnetic fields.

Electromagnetic field (EMF) treatment has proven to be effective against mineral scaling in water systems. Therefore, it should be assessed for the treatment of other deposits such as biofilms. In this study, a commercial device producing low-frequency EMF (1-10 kHz) was applied to a reactor fed with natural water for 45 days. The treatment promoted the concentration of microorganisms in suspension and limited the amount of sessile microorganisms in the biofilm, as determined by the measurement of total DNA, qPCR and microscopy. The structure of the bacterial community was assessed by t-RFLP and pyrosequencing analysis. The results showed that EMF treatment affected both planktonic and sessile community composition. EMFs were responsible for a shift in classes of Proteobacteria during development of the biofilm. It may be speculated that the EMF treatment affected particle solubility and/or microorganism hydration. This study indicated that EMFs modulated biofilm formation in natural water.

So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites.

This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity.

River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.

High temperature microbial activity in upper soil layers.

Biomineralization at high temperatures in upper soil layers has been largely ignored, although desertification and global warming have led to increasing areas of soils exposed to high temperatures. Recent publications evidenced thermophilic bacteria ubiquity in soils as viable cells, and their role in nutrient cycling and seedling development. High temperature events, frequently observed at medium and low latitudes, locate temporal niches for thermophiles to grow in soils. There, at temperatures inhibitory for common mesophiles, thermophilic bacteria could perform biogeochemical reactions important to the soil food web. Nutrient cycling analyses in soils at medium and low latitudes would benefit from considering the potential role of thermophiles.

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples.

The shift of microbial communities during a transition from mesophilic anaerobic digestion (MAD) to thermophilic anaerobic digestion (TAD) was characterized in two treatments. One treatment was inoculated with sludge and the other was inoculated with manure. In this study, methane was produced both in MAD and TAD, but TAD has slightly more methane produced than MAD. A broad phylogenetic spectrum of bacterial, archaeal, and fungal taxa at thermophilic conditions was detected. Coprothermobacter, Bacillus, Haloplasma, Clostridiisalibacter, Methanobacterium, Methanothermobacter, Saccharomycetales, Candida, Alternaria, Cladosporium, and Penicillium were found almost exclusively in TAD, suggesting their adaptation to thermophilic conditions and ecological roles in digesting the organic compounds. The characterization of the lesser-known fungal community revealed that fungi probably constituted an important portion of the overall community within TAD and contributed to this process by degrading complex organic compounds. The shift of the microbial communities between MAD and TAD implied that temperature drastically affected the microbial diversity in anaerobic digestion. In addition, the difference in microbial communities between sludge and manure indicated that different source of inoculum also affected the microbial diversity and community.