Sulfur oxidation in rice field soil: activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria

Indigenous mixotrophic aerobic denitrifiers stimulated by oxygen micro/nanobubble-loaded microporous biochar

The prevalence of hypoxia in surface sediment inhibits the growth of aerobic denitrifiers in natural waters. A novel oxygen micro/nanobubble-loaded microporous biochar (OMB) was developed to activate indigenous aerobic denitrifiers in this study. The results indicate a thin-layer OMB capping mitigates hypoxia effectively. Following a 30-day microcosm-based incubation, a 60 % decrease in total nitrogen concentration was observed, and the oxygen penetration depth in the sediment was increased from <4.0 mm to 38.4 mm. High-throughput sequencing revealed the stimulation of indigenous mixotrophic aerobic denitrifiers, including autotrophic denitrifiers such as Hydrogenophaga and Thiobacillus, heterotrophic denitrifiers like Limnobacter and unclassified_f_Methylophilaceae, and heterotrophic nitrification aerobic denitrification bacteria, including Shinella and Acidovorax, with total relative abundance reaching up to 38.1 %. Further analysis showed OMB enhanced the overall collaborative relationships among microorganisms and promoted the expression of nitrification- and denitrification-related genes. This study introduces an innovative strategy for stimulating indigenous aerobic denitrifiers in aquatic ecosystems.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

Plant-microbe eco-evolutionary dynamics in a changing world

Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.

Unravelling the interactive effect of soil and atmospheric mercury influencing mercury distribution and accumulation in the soil-rice system

Mercury (Hg) accumulation in rice is an emerging health concern worldwide. However, sources and interactions responsible for Hg species accumulation in different rice tissues are still uncertain. Four experimental plots were carefully designed at an artisanal Hg mining site and a control site to evaluate the effect of atmospheric and soil Hg contents on Hg accumulation in rice. We showed that inorganic Hg (IHg) contents in rice tissues grown either in contaminated or control site soil (non-contaminated soil) were higher at Hg artisanal mining site than those at the control site. Elevated total gaseous mercury (TGM) levels in ambient air were the predominant source of IHg to rice at the Hg mining area. Methylmercury (MeHg) concentrations in rice plant tissues increased in proportionality with MeHg contents in paddy soil. Our results suggest that both atmosphere and soil Hg sources have been impacted the IHg accumulation in rice. Above ground rice tissues, grains, leaves, and stalk accumulated IHg from both atmosphere and soil to varying degrees. Nonetheless, the study also provides the first direct evidence that atmospheric Hg accumulated by above-ground rice tissues could be translocated to below-ground tissues (roots). However, the extent to which atmosphere or soil Hg contributes to IHg in rice tissues may vary with each source's concentration gradient at the given site. No evidence of in planta Hg methylation was found during the current study. Hence, paddy fields are potential MeHg production sites, whereas paddy soil is a unique MeHg accumulation source in rice plants. This study expands and clarifies the contribution of various sources involved in Hg accumulation in the soil rice system. The findings here provide the basis for future research strategies to deal with the global issue of Hg contaminated rice.

Potential Implications of Interactions between Fe and S on Cereal Fe Biofortification

Iron (Fe) and sulfur (S) are two essential elements for plants, whose interrelation is indispensable for numerous physiological processes. In particular, Fe homeostasis in cereal species is profoundly connected to S nutrition because phytosiderophores, which are the metal chelators required for Fe uptake and translocation in cereals, are derived from a S-containing amino acid, methionine. To date, various biotechnological cereal Fe biofortification strategies involving modulation of genes underlying Fe homeostasis have been reported. Meanwhile, the resultant Fe-biofortified crops have been minimally characterized from the perspective of interaction between Fe and S, in spite of the significance of the crosstalk between the two elements in cereals. Here, we intend to highlight the relevance of Fe and S interrelation in cereal Fe homeostasis and illustrate the potential implications it has to offer for future cereal Fe biofortification studies.

Effects of water level and vegetation on nitrate dynamics at varying sediment depths in laboratory-scale wetland mesocosms

Recent increases in the frequency of extreme floods and droughts associated with climate change can affect fluctuating groundwater or wetland water levels and wetland plant growth, and consequently cause redox condition changes in nitrogen dynamics in wetland sediments. Here, we studied the fate of nitrate (NO₃^-), dissolved organic carbon (DOC), and the microbial characteristics at different sediment depths in response to water levels (i.e., 5 or 2.5 cm) above the sediment surface and in the presence or absence of plants (Phragmites communis Trin) for four months in three wetland mesocosms. Results showed that mesocosm A (MA) with a high water level (5 cm above the surface) and plants had significantly higher DOC concentrations (17.57 ± 8.22 mg/L) in sediment that were actively consumed by microorganisms than other mesocosms with low water level (MB) and without plant (MC) (8.77 ± 2.38 mg/L and 7.87 ± 2.72 mg/L in MB and MC, respectively). Consequently, the most of influent NO₃^- (20 mg-N/L) dramatically reduced in the vicinity of plant roots (-20 to -15 cm sediment depth) where active denitrification was expected in MA. Moreover, the functional genes involved in denitrification such as narG (2.4 × 10⁸ -3.5 × 10⁸ copies·g^-1) and nirS (5.6 × 10⁶-1.1 × 10⁷ copies·g^-1) were more abundant in this mesocosm. The profile of the microbial community structure at the class level revealed that Alphaproteocbacteria (MA: 14.19 ± 1.19%; MB: 14.01 ± 0.51%; MC: 15.21 ± 2.76%) and Actinobacteria (MA: 8.21 ± 1.91%; MB: 13.91 ± 2.13%; MC: 11.75 ± 3.43%) were predominant in all three mesocosms. Interestingly, the clustered heatmap supported the obvious difference in microbial composition of MA from other mesocosms showing relatively more abundant Clostridia (6.71 ± 1.54%) and Deltaproteobacteria (7.05 ± 0.68%). These results can provide an insight to understand the biogeochemical nitrogen cycle associated with climate change in wetland systems.

Draft Genome Sequence of Xanthobacter tagetidis ATCC 700314 T

Xanthobacter tagetidis is a thiophene-degrading bacterium associated with root balls of the plant genus Tagetes , which includes marigolds. It is a Gram-negative facultatively autotrophic bacterium with pleomorphic morphology exhibiting bent and branching rods. From strain TagT2C T (= ATCC 700314 T ), we report a genome assembly of 4,945,221 bp and a 69.5% G+C content.

Variation of the Bacterial Community in the Rhizoplane Iron Plaque of the Wetland Plant Typha latifolia

The survival of wetland plants in iron, sulfur and heavy metals-rich mine tailing ponds has been commonly attributed to the iron plaque (IP) on the root surface that acts as a protective barrier. However, the contribution of bacteria potentially regulates the iron-sulfur cycle and heavy metal exclusion at the root surface has not been studied in depth, particularly from a microbial ecology perspective. In this study, a pot experiment using Typha latifolia, a typical wetland plant, in non-polluted soil (NP) and tailing soil (T) was conducted. Samples from four zones, comprising non-rhizosphere soil (NR), rhizosphere soil (R) and internal (I) and external (E) layers of iron plaque, were collected from the NP and T and analyzed by 16S rRNA sequencing. Simpson index of the genus level showed greater diversities of bacterial community in the NP and its I zone is the most important part of the rhizosphere. PICRUSt predicted that the I zones in both NP and T harbored most of the functional genes. Specifically, functional genes related to sulfur relay and metabolism occurred more in the I zone in the T, whereas those related to iron acquisition and carbon and nitrogen circulation occurred more in the I zone in the NP. Analysis of dominant bacterial communities at genus level showed highest abundance of heavy metal resistant genus Burkholderia in the E zones in both soils, indicating that heavy metal resistance of Typha latifolia driven by Burkholderia mainly occurred at the external layer of IP. Moreover, many bacterial genera, such as Acidithiobacillus, Ferritrophicum, Thiomonas, Metallibacterium and Sideroxydans, involved in iron and sulfur metabolisms were found in the T and most showed higher abundance in the I zone than in the other zones. This work, as the first endeavor to separate the iron plaque into external and internal layers and investigate the variations of the bacterial communities therein, can provide an insight for further understanding the survival strategy of wetland plants, e.g., Typha latifolia, in extreme environment.

Spatial distributions of hexachlorobutadiene in agricultural soils from the Yangtze River Delta region of China

Hexachlorobutadiene (HCBD) is one of the persistent organic pollutants (POPs) listed by the Stockholm Convention and poses potential risks to human health and ecosystems. To reveal the regional-scale pollution status of HCBD in agricultural soils from fast-developing areas, an extensive investigation was conducted in the core Yangtze River Delta (YRD), China. The detectable concentrations of HCBD in 241 soil samples ranged from 0.07 to 8.47 ng g^-1 dry weight, with an average value of 0.32 ng g^-1 and a detection rate of 59.3%. Industrial emissions and intensive agricultural activities were the potential source of HCBD. The concentrations of HCBD were highly associated with the soil physicochemical properties such as organic matter contents. Higher concentrations of HCBD were found in paddy fields than other land-use types. The concentrations of HCBD were much lower than those of organochlorine pesticides and polychlorinated biphenyls. Significant positive correlations were found between HCBD and most organochlorine pesticides. HCBD was not found in ten vegetable samples due to its low concentration and detection rate. A positive relationship was observed between the level of HCBD and the biomass of fungi, indicating that the fungi in soils might be influenced by the existence of HCBD. The potential risks of HCBD to ecosystems and health of inhabitants were estimated to be negligible. The finding from this study provides an important basis for soil quality assessment and risk management of HCBD in China.

Characterization of sulfur oxidizing bacteria related to biogenic sulfuric acid corrosion in sludge digesters

BACKGROUND

Biogenic sulfuric acid (BSA) corrosion damages sewerage and wastewater treatment facilities but is not well investigated in sludge digesters. Sulfur/sulfide oxidizing bacteria (SOB) oxidize sulfur compounds to sulfuric acid, inducing BSA corrosion. To obtain more information on BSA corrosion in sludge digesters, microbial communities from six different, BSA-damaged, digesters were analyzed using culture dependent methods and subsequent polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). BSA production was determined in laboratory scale systems with mixed and pure cultures, and in-situ with concrete specimens from the digester headspace and sludge zones.

RESULTS

The SOB Acidithiobacillus thiooxidans, Thiomonas intermedia, and Thiomonas perometabolis were cultivated and compared to PCR-DGGE results, revealing the presence of additional acidophilic and neutrophilic SOB. Sulfate concentrations of 10-87 mmol/L after 6-21 days of incubation (final pH 1.0-2.0) in mixed cultures, and up to 433 mmol/L after 42 days (final pH <1.0) in pure A. thiooxidans cultures showed huge sulfuric acid production potentials. Additionally, elevated sulfate concentrations in the corroded concrete of the digester headspace in contrast to the concrete of the sludge zone indicated biological sulfur/sulfide oxidation.

CONCLUSIONS

The presence of SOB and confirmation of their sulfuric acid production under laboratory conditions reveal that these organisms might contribute to BSA corrosion within sludge digesters. Elevated sulfate concentrations on the corroded concrete wall in the digester headspace (compared to the sludge zone) further indicate biological sulfur/sulfide oxidation in-situ. For the first time, SOB presence and activity is directly relatable to BSA corrosion in sludge digesters.

Methylmercury varies more than one order of magnitude in commercial European rice

Rice is known to accumulate methylmercury (MeHg) in the rice grains. MeHg as a neurotoxin impacts on the human central nervous systems and especially on the developing brain. In this exploratory study, 87 commercial rice products sold in Europe, including nine baby-rice products, were analyzed for total Hg and MeHg content. MeHg concentration in all rice products investigated range from 0.11 to 6.45μgkg(-1) with an average value of 1.91±1.07μgkg(-1) and baby-rice is not significantly different from other rice products. Total Hg ranges from 0.53 to 11.1μgkg(-1) with an average of 3.04±2.07μgkg(-1). MeHg concentrations in all rice products studied in this work would not exceed the provisional tolerable weekly intake (PTWI). 30% of all commercial market rice products exceeded 10% of the PTWI calculated for toddlers or 13% of products for adults with rice based diet.

Influence of organic matters on AsIII oxidation by the microflora of polluted soils

The global AsIII-oxidizing activity of microorganisms in eight surface soils from polluted sites was quantified with and without addition of organic substrates. The organic substances provided differed by their nature: either yeast extract, commonly used in microbiological culture media, or a synthetic mixture of defined organic matters (SMOM) presenting some common features with natural soil organic matter. Correlations were sought between soil characteristics and both the AsIII-oxidizing rate constants and their evolution in accordance with inputs of organic substrates. In the absence of added substrate, the global AsIII oxidation rate constant correlated positively with the concentration of intrinsic organic matter in the soil, suggesting that AsIII-oxidizing activity was limited by organic substrate availability in nutrient-poor soils. This limitation was, however, removed by 0.08 g/L of added organic carbon. In most conditions, the AsIII oxidation rate constant decreased as organic carbon input increased from 0.08 to 0.4 g/L. Incubations of polluted soils in aerobic conditions, amended or not with SMOM, resulted in short-term As mobilization in the presence of SMOM and active microorganisms. In contrast, microbial AsIII oxidation seemed to stabilize As when no organic substrate was added. Results suggest that microbial speciation of arsenic driven by nature and concentration of organic matter exerts a major influence on the fate of this toxic element in surface soils.

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community

Rice paddies are indispensable for human food supply but emit large amounts of the greenhouse gas methane. Sulfur cycling occurs at high rates in these water-submerged soils and controls methane production, an effect that is increased by sulfate-containing fertilizers or soil amendments. We grew rice plants until their late vegetative phase with and without gypsum (CaSO4 ·2H2 O) amendment and identified responsive bacteria by 16S rRNA gene amplicon sequencing. Gypsum amendment decreased methane emissions by up to 99% but had no major impact on the general phylogenetic composition of the bacterial community. It rather selectively stimulated or repressed a small number of 129 and 27 species-level operational taxonomic units (OTUs) (out of 1883-2287 observed) in the rhizosphere and bulk soil, respectively. Gypsum-stimulated OTUs were affiliated with several potential sulfate-reducing (Syntrophobacter, Desulfovibrio, unclassified Desulfobulbaceae, unclassified Desulfobacteraceae) and sulfur-oxidizing taxa (Thiobacillus, unclassified Rhodocyclaceae), while gypsum-repressed OTUs were dominated by aerobic methanotrophs (Methylococcaceae). Abundance correlation networks suggested that two abundant (>1%) OTUs (Desulfobulbaceae, Rhodocyclaceae) were central to the reductive and oxidative parts of the sulfur cycle.

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Health risk and significance of mercury in the environment

Mercury (Hg) has long been recognised as a global pollutant, because it can remain in the atmosphere for more than 1 year. The mercury that enters the environment is generally acknowledged to have two sources: natural and anthropogenic. Hg takes three major forms in the environment, namely methyl-Hg (MeHg), Hg(0) and Hg(2+). All three forms of Hg adversely affect the natural environment and pose a risk to human health. In particular, they may damage the human central nervous system, leading to cardiovascular, respiratory and other diseases. MeHg is bioavailable and can be bioaccumulated within food webs. Therefore, several methods of eliminating Hg from the soil and the aquatic system have been proposed. The focus of this article is on phytoremediation, as this technique provides a low-cost and environmentally friendly alternative to traditional methods.

Rice methylmercury exposure and mitigation: a comprehensive review

Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.

Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella

The highly diverse and metabolically versatile microbial communities found in soil environments are major contributors to the global carbon, nitrogen, and sulfur cycles. We have used a combination of genome -based pathway analysis with proteomics and gene expression studies to investigate metabolic adaptation in a representative of these bacteria, Starkeya novella, which was originally isolated from agricultural soil. This bacterium was the first facultative sulfur chemolithoautotroph that was isolated and it is also able to grow with methanol and on over 39 substrates as a heterotroph. However, using glucose, fructose, methanol, thiosulfate as well as combinations of the carbon compounds with thiosulfate as growth substrates we have demonstrated here that contrary to the previous classification, S. novella is not a facultative sulfur chemolitho- and methylotroph, as the enzyme systems required for these two growth modes are always expressed at high levels. This is typical for key metabolic pathways. In addition enzymes for various pathways of carbon dioxide fixation were always expressed at high levels, even during heterotrophic growth on glucose or fructose, which suggests a role for these pathways beyond the generation of reduced carbon units for cell growth, possibly in redox balancing of metabolism. Our results then indicate that S. novella, a representative of the Xanthobacteraceae family of methylotrophic soil and freshwater dwelling bacteria, employs a mixotrophic growth strategy under all conditions tested here. As a result the contribution of this bacterium to either carbon sequestration or the release of climate active substances could vary very quickly, which has direct implications for the modeling of such processes if mixotrophy proves to be the main growth strategy for large populations of soil bacteria.

Enhanced transformation of diphenylarsinic acid in soil under sulfate-reducing conditions

Diphenylarsinic acid (DPAA) is known to be the major contaminant in soils where diphenylchloroarsine and diphenylcyanoarsine were abandoned after World Wars I and II. In this study, experimental model studies were performed to elucidate key factors regulating the transformation of DPAA under anaerobic soil conditions. The elimination of DPAA in Gleysol soils (Qiqihar and Shindori soils) was more rapid than in Mollisol and Regosol soils (Heihe and Ikarashi soils, respectively) during a 5-week incubation. No clear relationship between decreasing rates of DPAA concentrations and soil Eh values was found. The Ikarashi soil showed the slowest decrease in DPAA concentrations among the four soils, but the transformation of DPAA was notably enhanced by addition of exogenous sulfate together with acetate, cellulose or rice straw. Addition of molybdate, a specific inhibitor of sulfate reduction, resulted in the stagnation of DPAA transformation, suggesting that indigenous sulfate reducers play a role in DPAA transformation under anaerobic conditions. Arsenate, phenylarsonic acid, phenylmethylarsinic acid, diphenylmethylarsine oxide and three unknown compounds were detected as metabolites of DPAA. This is the first study to reveal enhancement of DPAA transformation under sulfate-reducing conditions.

Assessment of environmental mercury discharge at a four-year-old artisanal gold mining area on Lombok Island, Indonesia

Indonesian artisanal and small-scale gold mining activities (ASGM) have been described for the islands of Borneo (Kalimantan) and Sulawesi. But the increased gold price over recent years has seen operations extend to the islands of Lombok and Sumbawa. For the current research, an environmental assessment was conducted across three new ASGM locations. Gold is recovered by miners through a two-stage process of whole-ore amalgamation and cyanidation. Waste (tailings) is discharged to land or sea with no concern for contaminants in the tailings. The gold grade of ore is up to 5000 mg kg(-1). The mean gold grade of the amalgamation tailings is 7 mg kg(-1), dropping to 1.2 mg kg(-1) for the cyanidation tailings. The mean mercury concentration of the amalgamation tailings is about 3000 mg kg(-1) and greater than 1600 mg kg(-1) for the cyanidation tailings. Samples of paddy rice grain collected adjacent to cyanidation tailings ponds showed methyl mercury concentrations greater than 100 ng g(-1). This is five times above the Chinese permissible level for total mercury in food crops. The mean total mercury concentration in hair of Lombok ASGM workers was greater than that in a non-exposed population; however there was no difference in methyl mercury concentration. This indicates the primary pathway of mercury exposure is inhalation of volatile mercury in the atmosphere. Future exposure may come from ingestion of methyl mercury contaminated rice where discharge of cyanide tailings to paddies continues. To protect the environment and to enhance the sustainability of ASGM, appropriate tailings management must be implemented. The gold grade of the tailings indicates that the residual value might be recoverable with appropriate technology. Ongoing research is investigating systems such as phytoextraction that might assist ASGM operators in Lombok and Sumbawa to improve their environmental performance.

Spatial trend and pollution assessment of total mercury and methylmercury pollution in the Pearl River Delta soil, South China

Total mercury (THg) and methylmercury (MeHg) were measured in large number of soil samples collected from areas with different types of land use, different depth in the Pearl River Delta (PRD) of South China. THg and MeHg concentrations ranged from 16.7 to 3320ngg(-1) and 0.01 to 1.34ngg(-1), respectively. THg levels are highest in the top 0-20cm soil layer, and decrease from the surface to bottom layer soil. Spatial variation was observed with different types of land use. Urban parks had the highest concentrations and the other areas tended to decrease in the order of residential areas, industrial areas, vegetable fields, cereal fields, and woodlands. Temporal variation was also noted, and two relatively high THg contamination zones located in the northwestern part of the PRD have significantly expanded over the last two decades. Both THg and MeHg concentrations were correlated significantly with soil organic matter (OM), but not with soil pH. THg pollution status was evaluated using two assessment methods.

Synthesis of current data for Hg in areas of geologic resource extraction contamination and aquatic systems in China

China has become the largest contributor of anthropogenic atmospheric mercury (Hg) in the world owing to its fast growing economy and the largest of populations. Over the last two decades, Hg has become of increasing environmental concern in China and much has been published on its distribution, transportation, methylation, and bioaccumulation in aquatic systems and areas of geologic resource extraction contaminated sites, such as coal-fired power plants, non-ferrous smelters, Hg mining and retorting sites, Au amalgam, landfills, chemical plants, etc.. Environmental compartments, like soil, water, air, and crop from areas of geologic resource extraction contamination, especially from Hg mining regions, exhibit elevated values of total-Hg and MMHg. Risk assessments indicate that the consumption of rice, which has a high bioaccumulation of MMHg, has become the dominant pathway of MMHg exposure of inhabitants living in Hg mining areas. Low concentrations less than 5ngl(-1) in total-Hg can be observed in rivers from remote areas, however, high concentrations that reached 1600ngl(-1) in total-Hg can be found in rivers from industrial and urban areas. The studies of hydropower reservoirs of southwest China indicated the old reservoirs act as net sinks for total-Hg and net sources of MMHg, while newly established ones act as net sinks for both total-Hg and MMHg, which is in sharp contrast to the evolution of biomethylation in reservoirs established in the boreal belt of North America and Eurasia. Fish from those reservoirs have relatively low levels of total-Hg, which do not exceed the maximum total-Hg limit of 0.5mgkg(-1) recommended by WHO. Currently, however, there is still a large data gap regarding Hg even in the areas mentioned above in China, which results in poor understanding of its environmental biogeochemistry. Moreover, for a better understanding of human and environmental health effects caused by the fast growing economy, long-term Hg monitoring campaigns are urgently needed.

The process of methylmercury accumulation in rice (Oryza sativa L.)

Recent studies have shown that rice consumption can be an important pathway of methylmercury (MeHg) exposure to humans in Hg mining areas and also in certain inland areas of Southwestern China. The seed of rice has the highest ability to accumulate MeHg compared to other tissues. The main objective of this study was to investigate the process of (MeHg) accumulation in rice seed (Oryza sativa L.) by monitoring MeHg levels in specific tissues of rice plants experiencing various levels of Hg multisource pollution during a full rice growing season. Four groups of experimental plantations were utilized, distributed among a rural artisanal Hg production site and a regional background control site. Our results suggest that the newly deposited Hg is more readily transformed to MeHg and accumulated in rice plants than Hg forms with an extended residence time in soil, and soil is the potential source of MeHg in the tissues of rice plants. MeHg in soil was first absorbed by roots and then translocated to the above-ground parts (leaf and stalk). During the full rice growing season only a very small amount of MeHg was retained in the root section. In the premature plant, the majority of MeHg is located in the leaf and stalk; however, most of this MeHg was transferred to seed during the ripening period.

Enhancement of copper availability and microbial community changes in rice rhizospheres affected by sulfur

The role of sulfur on the availability of Cu and the bacterial community in rice rhizospheres was investigated by pot experiments. With sulfur addition, pH in rhizosphere soil decreased and Mg(NO₃)₂ extractable Cu increased significantly. The bacterial community composition also changed with sulfur addition. Some specific clones having high similarity to Thiobacillus, which indicated that sulfur oxidation in the rice rhizosphere could increase the availability of Cu. These results suggested that sulfur source which could provide substrate to sulfur oxidizing bacteria and enhance the availability of Cu was not a suitable sulfur fertilizer for Cu polluted soil.

In inland China, rice, rather than fish, is the major pathway for methylmercury exposure

BACKGROUND

Fish consumption is considered the primary pathway of methylmercury (MeHg) exposure for most people in the world. However, in the inland regions of China, most of the residents eat little fish, but they live in areas where a significant amount of mercury (Hg) is present in the environment.

OBJECTIVES

We assessed concentrations of total Hg and MeHg in samples of water, air, agricultural products, and other exposure media to determine the main exposure pathway of Hg in populations in inland China.

METHODS

We selected Guizhou Province for our study because it is highly contaminated with Hg and therefore is representative of other Hg-contaminated areas in China. We selected four study locations in Guizhou Province: three that represent typical environments with severe Hg pollution [due to Hg mining and smelting (Wanshan), traditional zinc smelting (recently closed; Weining), and heavy coal-based industry (Qingzhen)], and a village in a remote nature reserve (Leigong).

RESULTS

The probable daily intake (PDI) of MeHg for an adult population based on 60 kg body weight (bw) was considerably higher in Wanshan than in the other three locations. With an average PDI of 0.096 microg/kg bw/day (range, 0.015-0.45 microg/kg bw/day), approximately 34% of the inhabitants in Wanshan exceeded the reference dose of 0.1 microg/kg bw/day established by the U.S. Environmental Protection Agency. The PDI of MeHg for residents in the three other locations were all well below 0.1 microg/kg bw/day (averages from 0.017 to 0.023 microg/kg bw/day, with a maximum of 0.095 microg/kg bw/day). In all four areas, rice consumption accounted for 94-96% of the PDI of MeHg.

CONCLUSION

We found that rice consumption is by far the most important MeHg exposure route; however, most of the residents (except those in Hg-mining areas) have low PDIs of MeHg.

Bioaccumulation of methylmercury versus inorganic mercury in rice (Oryza sativa L.) grain

Mercury (Hg) bioaccumulation in aquatic food webs has been much studied, motivated from high Hg levels found in many fish species important for human consumption. Hg bioaccumulation in terrestrial food chains have received little attention and assumed to be of minor importance. However, recent studies showed that rice can be an important pathway of methylmercury (MeHg) exposure to inhabitants in Hg mining areas in China. In this study, 59 sampling sites (including 32 sites from "heavily polluted area", 19 from "less-impacted area" and 8 from "control sites") were selected in a Hg mining area in China and both inorganic Hg (IHg) and MeHg were determined in rice grain (brown rice) and soil samples to evaluate Hg bioaccumulation in rice grain. Bio-Accumulation Factors (BAFs) for IHg ranged from 0.00014 to 0.51 and from 0.71 to 50 for MeHg. BAFs for MeHg were on average more than 800 times higher than those for IHg (maximum: 40,000 times). This study, for the first time, showed that rice grain is an intensive bioaccumulator of MeHg, but not of IHg, which may be trapped by the roots.

Identification and characterization of sulfur-oxidizing bacteria in an artificial wetland that treats wastewater from a tannery

Wastewater from tanneries contains high concentrations of organic matter, chromium, nitrogen, and sulfur compounds. In this study, an artificial wetland is is used as the tertiary treatment in a tannery in León Gto., México. It consists of three subplots with an area of about 450 m2. Two subplots were planted with Typha sp. and the third with Scirpus americanus. Geochemical analyses along the flowpath of the wetland show that contaminants were effectively attenuated. The most probable number technique was used to determine rhizospheric microbial populations involved in the sulfur cycle and suggested that there were 104-10(6) cells g(-1) sediment of sulfate-reducing bacteria and 10(2)-10(5) of sulfur-oxidizing bacteria (SOB). Representatives of SOB were isolated on media containing thiosulfate. Phylogenetic analysis of 16S rRNA of SOB isolates shows that they belong to the genera Acinetobacter, Alcaligenes, Ochrobactrum, and Pseudomonas. Most of the isolates are organotrophic and can oxidize reduced sulfur compounds such as elemental sulfur or thiosulfate, accumulating thiosulfate, or tetrathionate during growth. All isolates can use reduced-sulfur compounds as their sole sulfur source and some can use nitrate as an electron acceptor to grow anaerobically. Our results illustrate the relevance of SOB in the functioning of the wetland constructed for tannery wastewater remediation.

Novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates

The microbial community and sulfur oxygenase reductases of metagenomic DNA from bioreactors treating gold-bearing concentrates were studied by 16S rRNA library, real-time polymerase chain reaction (RT-PCR), conventional cultivation, and molecular cloning. Results indicated that major bacterial species were belonging to the genera Acidithiobacillus, Leptospirillum, Sulfobacillus, and Sphingomonas, accounting for 6.3, 66.7, 18.8, and 8.3%, respectively; the sole archaeal species was Ferroplasma sp. (100%). Quantitative RT-PCR revealed that the 16S rRNA gene copy numbers (per gram of concentrates) of bacteria and archaea were 4.59 x 10(9) and 6.68 x 10(5), respectively. Bacterial strains representing Acidithiobacillus, Leptospirillum, and Sulfobacillus were isolated from the bioreactors. To study sulfur oxidation in the reactors, pairs of new PCR primers were designed for the detection of sulfur oxygenase reductase (SOR) genes. Three sor-like genes, namely, sor (Fx), sor (SA), and sor (SB) were identified from metagenomic DNAs of the bioreactors. The sor (Fx) is an inactivated SOR gene and is identical to the pseudo-SOR gene of Ferroplasma acidarmanus. The sor (SA) and sor (SB) showed no significant identity to any genes in GenBank databases. The sor (SB) was cloned and expressed in Escherichia coli, and SOR activity was determined. Quantitative RT-PCR determination of the gene densities of sor (SA) and sor (SB) were 1,000 times higher than archaeal 16S rRNA gene copy numbers, indicating that these genes were mostly impossible from archaea. Furthermore, with primers specific to the sor (SB) gene, this gene was PCR-amplified from the newly isolated Acidithiobacillus sp. strain SM-1. So far as we know, this is the first time to determine SOR activity originating from bacteria and to document SOR gene in bioleaching reactors and Acidithiobacillus species.

Isolation, characterization, and ecology of cold-active, chemolithotrophic, sulfur-oxidizing bacteria from perennially ice-covered Lake Fryxell, Antarctica

Novel strains of obligately chemolithoautotrophic, sulfur-oxidizing bacteria have been isolated from various depths of Lake Fryxell, Antarctica. Physiological, morphological, and phylogenetic analyses showed these strains to be related to mesophilic Thiobacillus species, such as T. thioparus. However, the psychrotolerant Antarctic isolates showed an adaptation to cold temperatures and thus should be active in the nearly freezing waters of the lake. Enumeration by most-probable-number analysis in an oxic, thiosulfate-containing medium revealed that the sulfur-oxidizing chemolithotroph population peaks precisely at the oxycline (9.5 m), although viable cells exist well into the anoxic, sulfidic waters of the lake. The sulfur-oxidizing bacteria described here likely play a key role in the biogeochemical cycling of carbon and sulfur in Lake Fryxell.

The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.

Quantification of Gram-negative sulphate-reducing bacteria in rice field soil by 16S rRNA gene-targeted real-time PCR

For the quantification of Gram-negative sulphate reducers in rice fields, 11 real-time PCR assays were established targeting 16S rRNA genes combined with SybrGreen detection. Three of these assays were specific for the "main" groups, i.e. the Desulfovibrionaceae, the Desulfobacteraceae and Desulfobulbus sp., whereas eight assays were developed for subgroups within the first two main groups. The detection limits of the assays were between 2 x 10(5) and 4 x 10(3) targets g(-1) (wet weight) or less than 0.02% of the eubacterial 16S rDNA targets in bulk soil, rhizosphere soil and rice root DNA extracts. Analysis of soil spiked with defined cell numbers of sulphate-reducing bacteria showed good correlation of measured target numbers to amended cells. In rice field bulk and rhizosphere soil, the Desulfobacteraceae were the predominant main group with target numbers of 6.4 x 10(7) (+/-1.0 x 10(7)) and 7.5 x 10(7) (+/-1.7 x 10(7)), respectively. Within this group the Desulforhabdus/Synthrophobacter assemblage and Desulfobacterium sp. were predominant. At the rice roots, the three main groups were abundant in similar numbers (approx. 1.0 x 10(8)) indicating that the relative abundance of the Desulfovibrionaceae and also of Desulfobulbus sp. was increased, relatively to the Desulfobacteraceae. Within the Desulfovibrionaceae the subgroup was predominant that was detected by assay DSV-II. This assay detects many from rice field soil isolated Desulfovibrio-strains and molecular retrieved sequences. Therefore these organisms that were already detected in the rice field environment by isolation and by molecular techniques are indeed best adapted to the conditions provided by the rice roots.

Bosea minatitlanensis sp. nov., a strictly aerobic bacterium isolated from an anaerobic digester

A strictly aerobic, mesophilic bacterium, strain AMX 51(T), was isolated from anaerobic digester sludge. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum. The isolate had phenotypic traits of the genus Bosea, including cellular fatty acid and substrate utilization profiles. Physiological characteristics and antibiotic susceptibility were determined. Phylogenetic analysis revealed that strain AMX 51(T) was a member of the alpha-Proteobacteria, most closely related to Bosea thiooxidans DSM 9653(T) (similarity of 98.88 %). Methylobacterium organophilum JCM 2833(T), Methylobacterium mesophilicum JCM 2829(T), Afipia clevelandensis DSM 7315(T), Afipia felis DSM 7326(T), Afipia broomeae DSM 7327(T), Blastobacter denitrificans LMG 8443(T) and Bradyrhizobium japonicum DSM 30131(T) showed significant 16S rRNA gene sequence similarities to strain AMX 51(T). The DNA G+C composition of strain AMX 51(T) was 68.5 mol%. DNA-DNA hybridization analysis revealed 44.2 and 15.1 % relatedness between strain AMX 51(T) and the respective type strains of Bosea thiooxidans and A. felis. Overall results suggest that strain AMX 51(T) (=DSM 13099(T)=ATCC 700918(T)=CIP 106457(T)) represents a novel species of the genus Bosea; the name Bosea minatitlanensis sp. nov. is proposed.

Isolation and Molecular Characterization of Thiosulfate-oxidizing Bacteria from an Italian Rice Field Soil

In rice paddy soils an active cycling of sulfur compounds takes place. To elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. From the MPN enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. These strains were characterized by 16S rDNA analyses. The isolates were affiliated to seven different phylogenetic groups within the alpha- and beta-subclass of Proteobacteria. Two of these phylotypes were already described as S-oxidizers in this environment (Xanthobacter sp. and Bosea sp. related strains), but five groups represented new S-oxidizers in rice field soil. These isolates were closely related to Mesorhizobium loti, to Hydrogenophaga sp., to Delftia sp., to Pandoraea sp. or showed sequence similarity to a strain of Achromobacter sp.

Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice field soil by real-time PCR with SybrGreen detection

Real-time PCR is a new and highly sensitive method for the quantification of microbial organisms in environmental samples. This work was conducted to evaluate real-time PCR with SybrGreen (SG) detection as quantification method for Desulfotomaculum lineage 1 organisms in samples of rice field soil. The method was optimized in several parameters like SG concentration. These allowed quantitative PCR with different primer combinations yielding PCR products with lengths up to 1066 bp and with sensitivities of 10(2) targets for all assays. The detection limit in environmental DNA extracts (rice bulk soil and rice roots) was 10(6) targets per gram dry weight according to the dilution of the DNA extracts necessary to overcome PCR inhibition of humic substances. A verification, that the fluorescence increase was due to specific PCR products, was done by agarose gel electrophoresis since melting curve analysis of the PCR products did not show a distinct peak in the first derivative, when the environmental DNA extracts were used in PCR. Amplification with a primer combination specific for Desulfotomaculum lineage 1 organisms showed an abundance of this group of approximately 2% and 0.5% of the eubacterial 16S rDNA targets in rice bulk soil and rice root samples, respectively. Approximately half of this number was obtained in both habitats with a PCR assay specific for a Desulfotomaculum sequence cluster obtained previously from rice field soil.

Methane oxidation and the competition for oxygen in the rice rhizosphere

A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O(2) with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a Methylocystis sp.) and heterotrophs (a Pseudomonas sp. and a Rhodococcus sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently < 5 microM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between Pseudomonas spp. and Methylocystis spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.

Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots

Specific PCR assays were used to amplify the 16S rRNA genes of the Desulfobacteriaceae and the Desulfovibrionaceae from extracted environmental DNA from rice roots. 16S rDNA-based community patterns of the Desulfobacteriaceae were generated via terminal restriction fragment length polymorphism analysis from rice roots and compared with bulk soil. The molecular fingerprints showed no significant difference between rice roots and bulk soil, but changes during the vegetation period. 16S rDNA clone libraries and sequencing showed that the predominant terminal restriction fragments represented distinct phylogenetic groups. The 16S rDNA clone sequences of the Desulfobacteriaceae fell in the phylogenetic radiation of Desulfonema and Desulfosarcina or grouped within the Desulforhabdus-Syntrophobacter assemblage. Three of the latter sequences were closely affiliated with the MPN isolate EZ-2C2 from rice roots. All Desulfovibrionaceae 16S rDNA clone sequences, with one exception, were affiliated with the MPN isolate F1-7b from rice roots. The clustering of the clone sequences and the close phylogenetic affiliation with isolates from MPN enrichments from the same habitat in two cases indicated that these sequence clusters may represent predominant Gram-negative sulfate reducers on rice roots. Quantification of the bacterial abundances was accomplished by rRNA dot blot hybridization. In total the Gram-negative sulfate reducers accounted for approximately 2-3% of the total rRNA content. The relative rRNA abundance of the Desulfobacteriaceae was, at 1.4%, higher than that of the Desulfovibrionaceae (0.5%).

Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation

The study of methane-oxidising bacteria (methanotrophs) is of special interest, because of their role in the natural reduction of methane emissions from many different sources. Therefore new probes were developed to detect specifically either type I (Methylococcaceae) or type II methanotrophs (Methylocystaceae). The probes have shown high specificity in fluorescence in situ hybridisations (FISH), as demonstrated by parallel hybridisation of target and reference strains as well as sequence data analysis. With these probes, methanotrophs were detected in soil and root samples from rice microcosms, demonstrating their applicability even in a complex environmental matrix.

Detection of Desulfotomaculum in an Italian rice paddy soil by 16S ribosomal nucleic acid analyses

Two specific primers were developed for the amplification of 16S rRNA genes of Desulfotomaculum lineage 1 to detect members of the genus Desulfotomaculum in rice field soil. The combination of both primers in PCR allowed the specific amplification and cloning of ten 16S rDNA sequences of this group from rice paddy soil DNA extracts. The phylogenetic analysis showed that these sequences formed a deeply branching cluster within Desulfotomaculum lineage 1, together with two sequences from the database and two sequences from a hydrocarbon-contaminated aquifer. Dissimilarity values to validly described species, including recently isolated strains of Desulfotomaculum from rice paddy microcosms, were higher than 12%. Within the new cluster the cloned sequences formed three separate groups which were each represented by at least two sequences with identities of >/=99% while one sequence represented an additional group. The sequences should represent sulfate-reducing organisms because they clearly fell into the physiologically coherent group of Gram-positive sulfate reducers. The relative abundance of bacteria of the Desulfotomaculum lineage 1 in rice paddy soil and root samples was estimated with rRNA dot blot hybridizations of extracted RNA. The relative RNA content of Desulfotomaculum lineage 1 was 0.55% in the bulk soil and 1% in the rice root samples, respectively, of the total 16S rRNA content (probe Eub338). Hybridization of rRNA with a probe targeting the new cluster represented by the cloned sequences confirmed the high abundance of 16S rRNA sequences from this cluster in the rice paddy field samples. Another hybridization probe detecting Desulfotomaculum acetoxidans and two closely related Desulfotomaculum isolates from rice paddy soil indicated that these bacteria were less abundant.

Sulfate-reducing bacteria in rice field soil and on rice roots

Rice plants that were grown in flooded rice soil microcosms were examined for their ability to exhibit sulfate reducing activity. Washed excised rice roots showed sulfate reduction potential when incubated in anaerobic medium indicating the presence of sulfate-reducing bacteria. Rice plants, that were incubated in a double-chamber (phylloshpere and rhizosphere separated), showed potential sulfate reduction rates in the anoxic rhizosphere compartment. These rates decreased when oxygen was allowed to penetrate through the aerenchyma system of the plants into the anoxic root compartment, indicating that sulfate reducers on the roots were partially inhibited by oxygen or that sulfate was regenerated by oxidation of reduced S-compounds. The potential activity of sulfate reducers on rice roots was consistent with MPN enumerations showing that H2-utilizing sulfate-reducing bacteria were present in high numbers on the rhizoplane (4.1 x 10(7) g-1 root fresh weight) and in the adjacent rhizosperic soil (2.5 x 10(7) g-1 soil dry weight). Acetate-oxidizing sulfate reducers, on the other hand, showed highest numbers in the unplanted bulk soil (1.9 x 10(6) g-1 soil dry weight). Two sulfate reducing bacteria were isolated from the highest dilutions of the MPN series and were characterized physiologically and phylogenetically. Strain F1-7b which was isolated from the rhizoplane with H2 as electron donor was related to subgroup II of the family Desulfovibrionaceae. Strain EZ-2C2, isolated from the rhizoplane on acetate, grouped together with Desulforhabdus sp. and Syntrophobacter wolinii. Other strains of sulfate-reducing bacteria originated from bulk soil of rice soil microcosms and were isolated using different electron donors. From these isolates, strains R-AcA1, R-IbutA1, R-PimA1 and R-AcetonA170 were Gram-positive bacteria which were affiliated with the genus Desulfotomaculum. The other isolates were members of subgroup II of the Desulfovibrionaceae (R-SucA1 and R-LacA1), were related to Desulforhabdus sp. (strain BKA11), Desulfobulbus (R-PropA1), or culstered between Desulfobotulus sapovorans and Desulfosarcina variabilis (R-ButA1 and R-CaprA1).