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

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

Diversity and Characterization of Potential H2-Dependent Fe(Ⅲ)-Reducing Bacteria in Paddy Soils

Microbial ferric iron reduction, with organic carbon or hydrogen as the electron donor, is one of the most important biogeochemical processes in anoxic paddy soils; however, the diversity and community structure of hydrogen-dependent dissimilatory iron-reducers remain unknown. Potential H2-dependent Fe(III)-reducing bacteria in paddy soils were explored using enrichment cultures with ferrihydrite or goethite as the electron acceptor and hydrogen as the electron donor. Terminal restriction fragment length polymorphism (T-RFLP) analysis and cloning/sequencing were conducted to reveal bacterial community structure. Results showed that Geobacter and Clostridium were the dominant bacteria in the enrichment cultures. Fe(III) oxide mineral phases showed a strong effect on the community structure; Geobacter and Clostridium were dominant in the ferrihydrite treatment, while Clostridium spp. were dominant in the goethite treatment. These suggested that H2-dependent Fe(III)-reducing bacteria might be widely distributed in paddy soils and that besides Geobacter, Clostridium spp. might also be an important group of H2-dependent Fe(III)-reducing microorganisms.     

Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils

Recent studies of ammonia-oxidizing archaea (AOA) suggested their significant contributions to global nitrogen cycling, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota. AOA are ubiquitous in terrestrial ecosystems, have unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirements compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers have been dramatically challenged, and the dominant nitrifying groups urgently called for re-assessment. Controversially, the relative contributions of AOA and AOB to autotrophic ammonia oxidation have been reported to vary in different soils, but ammonia substrate availability, which was largely restricted under acidic conditions, seemed to be the key driver. Theoretically predicted ammonia concentrations in acidic soils below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in ammonia-limited acidic environments. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeon, Nitrosotalea devanaterra. Here, we review the currently available knowledge concerning the history and progress in our understanding of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms of nitrification in nutrient-depleted acidic soils, present the possible mechanisms shaping the distinct niches of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in ammonia oxidation of acidic soils.     

Response of ammonia oxidizing archaea and bacteria to changing water filled pore space

This study examined the effect of water filled pore space (WFPS) on gross N fluxes and community structure and abundance of ammonia oxidizing archaea and bacteria in a semi-arid soil. Different WFPS altered the community structure of both AOA and AOB. Ammonia oxidizer communities (for both archaea and bacteria) from ‘wet’ soils (95, 85 and 75% WFPS) and ‘dry’ soils (25, 45 and 55% WFPS) were distinctly different from one another. Additionally there was a significant relationship between community structure and gross rates of nitrification. There was also a significant relationship between WFPS and bacterial amoA abundance but not archaeal amoA abundance suggesting that bacterial ammonia oxidizers are more responsive to changes in soil water availability. These results are in agreement with other studies suggesting that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches with consequences for nitrification in response to WFPS. Overall findings from this study indicate that nitrification, both in terms of process rates and populations responsible for nitrification activity, is highly responsive to soil water availability.     

不同品种水稻土壤氨氧化细菌和氨氧化古菌群落结构组成

本研究通过提取土壤总DNA,利用特异引物进行PCR扩增和变性梯度凝胶电泳(DGGE),研究了不同品种水稻对稻田土壤氨氧化细菌和氨氧化古菌群落结构组成的影响.结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌,且氨氧化古菌种类更多;不同品种水稻氨氧化细菌群落结构组成差异较大,其中以"天A/Km71"、"闽优1027"和"Km62/1027"3个品种相似性较高,且明显不同于其余3个品种:而氨氧化古菌群落结构组成在不同土层间表现出较大差异,其中以"天A/Km71"和"Km62/1027"的表土与根际土氨氧化古菌群落组成差异最大.研究表明不同水稻品种及土壤层次对氨氧化微生物群落结构组成具有一定影响,证明氨氧化微生物尤其是氨氧化古菌在稻田土壤生态系统中占有重要地位.     

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.     

Hormonal interactions in the rhizosphere of maize (Zea mays L.) and their effects on plant development

The phytohormones indole acetic acid (IAA), abscisic acid (ABA), isopentenyladenosine (iPA), dihydrozeatin riboside (DHZR), and zeatinriboside (ZR) were determined quantitatively using monoclonal antibodies by an enzyme immunoassay in the following samples: a) culture filtrates of known bacterial species, growing naturally in close, loose or without contact with higher plants; b) culture filtrates of heterogeneous populations of microorganisms, isolated from the rhizoplane and rhizosphere of maize as well as from root-free soil; c) sterile and nonsterile maize root exudates; d) in the rhizosphere of field-grown maize plants and in soil fractions distant from the roots (bulk soil). ABA was not detected in the culture filtrates of bacteria and ZR was not found in bulk soil and rhizosphere soil of field-grown maize. All phytohormones were present in the other samples analyzed. Bacterial cultures with cell concentrations roughly equal to those in the rhizosphere of field-grown maize may produce under optimal laboratory conditions phytohormone concentrations comparable to those measured in the rhizosphere of field-grown maize. During the whole vegetation period there was a steep phytohormone gradient in the first centimeter of soil around a maize root in the field. Inoculation of maize seedlings growing in nutrient solution with rhizosphere bacteria resulted in a synergistic increase in phytohormone concentration in comparison to the sum of hormone production by sterile plant roots and by bacteria cultures. Using regression analysis, the relationship between phytohormone concentration changes in the rhizosphere and different morphological characteristics of the maize plant were shown to be highly significant.     

Comparative diversity and abundance of ammonia monooxygenase genes in mulched and vegetated soils

Soil microbial habitats are altered by mulching, a common practice in urban areas during which vegetation is removed and soils covered to suppress weeds and retain moisture. Soil microorganisms drive nitrogen-cycling processes in mulched soils, because living plants no longer take up ammonium-N released during decomposition of residual organic matter. Because ammonia oxidizers carry out the first, rate-limiting step of nitrification, we compared ammonia oxidizers in experimental, unfertilized plots of mulched and vegetated soils. We hypothesized that mulched and vegetated soils would support contrasting communities of bacterial and archaeal ammonia oxidizers, as determined by quantitative PCR and primers specific for genes encoding ammonia monooxygenase subunit A (amoA). Clone libraries of archaeal amoA also were constructed to compare diversity in soil cores, duplicate blocked plots, and treatments (bark-mulched, gravel-mulched, and unmanaged old field vegetation). Gene copies from ammonia-oxidizing bacteria (AOB) ranged from 2.2 × 10⁶ to 2.7 × 10⁷ gene copies per gram dry soil and did not differ across treatments. In contrast, gene copies from ammonia-oxidizing archaea (AOA) ranged from 9.1 × 10⁵ to 1.0 × 10⁸ copies per gram dry soil, with bark-mulched soils having significantly lower abundance. Community structure of AOA in gravel-mulched soils was distinct from the other two treatments. At 97% amino acid similarity, 22 operational taxonomic units, or OTUs, were identified, with only one OTU found in all 18 clone libraries. This ubiquitous OTU-1, which was highly similar to published amoA sequences recovered from soils, comprised 55% of all 482 translated sequences. Greater variability in OTU richness was observed among cores from mulched soils than from vegetated soils. Our observations supported our hypothesis that AOA communities differ in mulched and vegetated soils, with mulched soils providing altered and variable microniches for these N cycling microorganisms.     

微白黄链霉菌对谷子萌发及拔节期生长的作用及机制

为探究外源放线菌对谷子种子萌发、拔节期植株生长的影响,本研究以一株微白黄链霉菌（Streptomyces albidoflavus）T4为供试菌株,以无菌水为对照,通过培养皿试验分析T4发酵液原液、10、100、1 000倍稀释液对谷子种子萌发的影响;以无菌剂添加处理作为对照,通过盆栽试验探究T4活菌制剂包衣和拌土对拔节期谷子植株生长及根际微生物的作用。结果表明,T4发酵液处理提高了谷子种子的萌发率,尤其以培养前期的提高幅度较大。T4发酵液的原液、10和100倍稀释液处理使谷子培养24 h后的萌发率与无菌水对照相比分别增加了5.8、6.7和9.2个百分点,100倍稀释液使谷子的发芽势、发芽指数和胚根长较对照分别提高了9.2个百分点、23.1%和13.4%。盆栽试验中,与无菌剂对照相比,包衣施加T4菌剂处理拔节期谷子地上植株生物量和根系生物量分别提高了22.5%和32.7%;根尖数和根分叉数分别增加了90.9%和66.9%;根际细菌（B）数量和微生物总数分别增加了95.1%和49.5%;真菌（F）数量减少了52.1%;放线菌（A）与真菌的数量比值（A/F）、细菌与真菌的数量比值（B/F）...     

Bt-transgenic rice straw affects the culturable microbiota and dehydrogenase and phosphatase activities in a flooded paddy soil

There have been few investigations of the possible effects of genetically engineered plants on the microbiota and enzyme activities in flooded soil. We studied the influence of the transgenic rice KeMingDao (KMD) straw on the culturable microbiota and enzymatic activities in a flooded paddy soil under laboratory conditions. KMD contained a synthetic cry1Ab gene from Bacillus thuringiensis under the control of a maize ubiquitin promoter and linked in tandem with the gusA and hpt genes. The results showed that there were only some occasional significant differences (P<0.05) in the number of Colony forming units of aerobic bacteria, actinomycetes and fungi and in the number of anaerobic fermentative bacteria, denitrifying bacteria, hydrogen-producing acetogenic bacteria, and methanogenic bacteria between the paddy soil amended with Bt-transgenic rice straw and with the non-Bt parental rice straw during the early stages of incubation. From d14 to d84 there were significant increases (P<0.05) in soil dehydrogenase and soil neutral phosphatase activity in soils amended with rice straw compared to soil without added straw. The dehydrogenase activity was significantly greatly (almost 1.95-fold) in soil amended with Bt-transgenic straw from d7 to d14 but from d21 to d49 there was significantly greater activity (about 1.47-fold) in the soil amended with non-Bt-straw. There were no apparent differences between the activity of soil neutral phosphatase in the soils to which non-Bt-straw and Bt-straw had been added. However, both soils to which rice straws were added demonstrated significant differences in the number of microorganisms except for aerobic bacteria and enzymatic activities with respect to the control soil throughout the incubation. The above results indicated that the Bt-straw from KMD transgenic rice is not toxic to a variety of culturable microorganisms in the studied flooded paddy soil.     

Distribution of Metabolically Active Prokaryotes (Archaea and Bacteria) throughout the Profiles of Chernozem and Brown Semidesert Soil

The distribution of metabolically active cells of archaea and bacteria in the profiles of typical chernozems (Voronezh oblast) and brown semidesert soils (Astrakhan oblast) of natural and agricultural ecosystems was studied using the method of fluorescent in situ hybridization (FISH). The studied soils differed sharply in the microbial biomass and in the numbers of metabolically active cells of archaea and bacteria. The number of active bacterial cells was 3.5–7.0 times greater than that of archaea. In the arable chernozem, the numbers of active cells of archaea and bacteria were 2.6 and 1.5 times, respectively, lower than those in the chernozem under the shelterbelt. The agricultural use of the brown semidesert soil had little effect on the abundances of bacteria and archaea. The soil organic carbon content was the major factor controlling the numbers of metabolically active cells of both domains. However, the dependence of the abundance of bacteria on the organic matter content was more pronounced. The decrease in the organic carbon and total nitrogen contents down the soil profiles was accompanied by the decrease in the bacteria: archaea ratio attesting to a better adaptation of archaea to the permanent deficiency of carbon and nitrogen. The bacteria: archaea ratio can serve as an ecotrophic indicator of the state of soil microbial communities.     

Nitrogen loading levels affect abundance and composition of soil ammonia oxidizing prokaryotes in semiarid temperate grassland

Purpose  

Global nitrogen deposition has profound impact on the terrestrial ecosystem including the semiarid temperate grassland, causing vegetation community shifts and soil acidification. Little is known regarding the effect of nitrogen (N) deposition on the belowground microbial communities. This study aimed to examine the response of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to added N in semiarid temperate grassland.     

Characteristics of soil microbiostasis

No increase in numbers of fungi, actinomycetes and bacteria in 3 days, as measured by selective media, was used as an indication of the presence of fungistasis, actinostasis and bacteriostasis in soil, respectively. The population of fungi, actinomycetes and bacteria did not increase in 9 of 10 soils tested indicating concurrent existence of fungistasis, actinostasis and bacteriostasis in a wide range of soils. When Penicillium funiculosum, Streptomyces scabies and Agrobacterium radiobacter were used as test organisms, these three types of microbiostasis were detected simultaneously in all 8 soils tested. All three groups of microorganisms flourished in autoclaved soil, and microbiostasis was restored to sterilized soil by reinoculation with 1% natural soil or microorganisms including antibiotic and non-antibiotic producers. Soil microbiostasis was annulled completely or partially by addition of different nutrie0nts. Bacteriostasis appeared to be the easiest to overcome with nutrients among these three types of microbiostasis.     

Effects of repeated drought on soil microarthropod communities in the northern Chihuahuan Desert

 Soil microarthropods were sampled in plots centered on creosotebushes (Larrea tridentata) and in plots centered on mesquite (Prosopis glandulosa) coppice dunes. Nine plots in each area were covered by rain-out shelters with greenhouse plastic roofs which excluded natural rainfall and nine plots received natural rainfall. There were differences in the abundance of several mite taxa in soils from the mesquite coppice dune plots. Some taxa (Stigmaeidae, Nanorchestidae, and Entomobryidae) occurred in significantly lower numbers in the soils of the drought plots. Other taxa (Tarsonemidae and Cunaxidae) were more abundant in the drought plots in the mesquite coppice dunes. There were no significant differences in the abundance of any of the dominant taxa of soil microarthropods in the drought and control plots centered on creosotebush. In the creosotebush habitat, there were significantly fewer Prostigmata in the plots exposed to drought. In an area with both creosotebush and mesquite, there were no significant differences in microarthropod population responses to drought and in recovery from drought. The differences in responses of soil microarthropods to drought in creosotebush and mesquite habitats are attributed to the differences in soil stability, litter accumulations, and microclimate associated with the shrubs. Received: 29 December 1997     

Replant diseases: Bacterial community structure and diversity in peach rhizosphere as determined by metabolic and genetic fingerprinting

Peach tree replant disease, though reported on in the literature for more than two centuries, has yet to have its causes clearly defined. Decline in peach productivity has been attributed to toxic agents, insects, nutritional disturbances, spray residues, fungi and nematodes. Bacteria has also been indicated as a contributing factor.Peach replant disease was reproduced by using two successive cultures on the same soil. Bacterial communities were isolated and characterized from healthy and diseased peach trees. The potential role of cyanide production by rhizobacteria in the replant problem of peaches was studied. Culture-dependent (evaluation of the number of culturable bacteria, metabolic activities, Biolog^® GN2) and independent (ribosomal intergenic spacer analysis, RISA) methods were used, in order to compare bacterial community structure and diversity in healthy and sick soils and to evaluate the possible role of cyanide.Bacterial densities were significantly increased in sick soils. Metabolic activities (Biolog^® GN2) and genetic structure, observed through RISA, were also significantly modified in sick soils. Changes in the composition of individual microbial groups in the rhizosphere of peach trees excavated from healthy or sick soil indicated the involvement of rhizobacteria in the etiology of the replant sickness of peach soil. More than 60% of the strains isolated from healthy soils corresponded to Pseudomonas sp. and 58% of the isolates from sick soils were Bacillus sp. This study determined that Bacillus were able to produce in vitro HCN. It also appeared that in sick soil, there was a shift in the structure of bacterial communities with an increase noted in phytotoxic microorganisms capable of producing HCN compounds.     

The structure of the bacterial heterotrophic block in tundra soils of Yamal Peninsula

The tundra cryogenic soils of Yamal Peninsula have a high pool of prokaryote microorganisms characteristic of ecosystems where the environmental conditions are unfavorable for microbiological processes. The lowering of the cultivation temperature from 20 to 5°C did not affect the number of bacteria and their taxonomic structure. Psychrotolerant gram-negative bacteria represented by oligotrophs and copiotrophs predominated in the bacterial communities. Among the bacteria of the hydrolytic block, only bacilli were isolated upon cultivation on the media. The species spectrum of the Bacillus genus was determined by the capability of its representatives for growth at low temperatures. The bacteria isolated from the cryogenic soils had a high nitrogenase activity, which increased under the lower cultivation temperature. This fact shows that the majority of the bacteria in tundra soils has adapted to functioning at low temperatures.     

Heavy metals and soil microbes

The discovery in the early 1980s that soil microorganisms, and in particular the symbiotic bacteria Rhizobium, were highly sensitive to heavy metals initiated a new line of research. This has given us important insights into a range of topics: ecotoxicology, bioavailability of heavy metals, the role of soil biodiversity, and the existence of ‘keystone’ organisms. Concurrently, and particularly in Europe, the research led to new approaches to the protection of soils from pollution that take into account the many effects on soil microorganisms. To date these key findings have largely been ignored in the USA, although our results caused considerable controversy there. In the past decade there have been many advances in the ecotoxicological assessment of metals and their effects on soil organisms but major gaps in knowledge and theory remain with regard to how microorganisms are exposed and respond to metals in soils. In this brief review we emphasise the need for long-term experiments and basic research to forge this understanding and improve environmental protection policies.     

Spatio-temporal variability of microbial abundance and community structure in the puddled layer of a paddy soil cultivated with wetland rice (Oryza sativa L.)

The puddled layer of paddy soils represents a highly dynamic environment regarding the spatio-temporal variability of biogeochemical conditions. To study these effects on the abundance and community structure of microbial populations, a rhizotron experiment was conducted throughout an entire growing season of wetland rice. Soil samples were taken from selected areas of the puddled layer (bulk soil, oxidized layer, rhizosphere) at main plant developmental stages such as (i) the initial stage, (ii) tillering, (iii) panicle initiation, (iv) flowering, and (v) maturity. Cell numbers of archaea, bacteria, and selected phyla were assessed by catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The structure and diversity of microbial communities was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) along with sequencing of selected bands. Following submergence of the paddy soil, shifts of bacterial community structure were observed in the oxidized layer and the rhizosphere. Members of the β-Proteobacteria became predominant in the rhizosphere at tillering stage and were affiliated with aerobic, iron-oxidizing bacteria of the genus Sideroxydans. Seasonal effects were mainly visible in the rhizosphere, as several phylogenetic subgroups including methanotrophic bacteria showed increased cell numbers at flowering stage. Cell numbers of methanogenic archaea were also highest at flowering stage (bulk soil, rhizosphere) and members of the Methanocellales were identified as predominant archaeal populations in areas of oxic and anoxic conditions. In contrast to bacteria, the communities of archaea in the puddled layer of the studied paddy soil were less influenced by spatio-temporal variations of biogeochemical conditions.     

Forms of phosphorus in bacteria and fungi isolated from two Australian soils

To understand the origin of organic and condensed forms of phosphorus (P) in soils, detailed information about P forms in microorganisms is required. We isolated 7 bacteria and 8 fungi from two Australian soils and analyzed the P forms in their pure cultures by extraction with NaOH-EDTA followed by ³¹P solution nuclear magnetic (NMR) spectroscopy. The bacteria belonged to the actinobacteria and the fungi to the ascomycota, as determined by rDNA sequencing. The proportions of broad forms of P were significantly different between the bacterial and fungal isolates (analysis of similarities, p = 0.001). Ortho-, pyro- and polyphosphate were present in higher proportions in fungi, while monoester and diester P were present in higher proportions in bacteria. Spectral deconvolution of the monoester region revealed 15 distinct resonances. The three major ones, which were identified by spiking experiments as glycerol 1-phosphate, glycerol 2-phosphate and adenosine-5′-monophosphate (AMP), comprised 56–74% of P in the monoester region. Ordination by principal component analysis and testing for treatment effects using analysis of similarities showed significant separation of P distribution in the monoester region between bacterial and fungal isolates (p = 0.007). However, neither group of microorganisms had a specific single P form which might be considered characteristic. As such, it may be difficult to distinguish soil P from bacterial or fungal origins, with the possible exception of a predominantly fungal origin of pyro- and polyphosphate. The identification of three major resonances in the monoester region of microorganisms is important, since the same resonances are found in ³¹P NMR spectra of soil extracts.     

Soils from the pensacola mountains,antarctica: Physical,chemical and biological characteristics

Additional information on the physical, chemical and microbiological properties of soils from the Pensacola Mountains, Antarctica is presented. The soils in this region, like those elsewhere in the frigid desert oases of Antarctica, were formed by physical and chemical weathering of igneous and metamorphic rocks. Soils from several collection sites contained primary clays. Free phosphate was undetectable at all sites but significant concentrations of N compounds, especially nonbiogenically formed NO^?₃, were present. Extractable chlorophyll a and adenosine triphosphate concentrations were below detection limits at all seven sites. All sites contained viable microorganisms: seven contained yeasts, six aerobic heterotrophic bacteria and four had algae. While some have suggested that Antarctic soils may be abiotic, this assertation needs re-evaluation in the light of new and improved techniques to culture and isolate viable microorganisms.