Haloarchaeal assimilatory nitrate-reducing communities from a saline alkaline soil

Assimilatory nitrate reduction (ANR) is a pathway wherein NO₃⁻ is reduced to NH₄⁺, an N species that can be incorporated into the biomass. There is little information about the ANR genes in Archaea and most of the known information has been obtained from cultivable species. In this study, the diversity of the haloarchaeal assimilatory nitrate-reducing community was studied in an extreme saline alkaline soil of the former lake Texcoco (Mexico). Genes coding for the assimilatory nitrate reductase ( narB ) and the assimilatory nitrite reductase ( nirA ) were used as functional markers. Primers to amplify and detect partial narB and nirA were designed. The analysis of these amplicons by cloning and sequencing showed that the deduced protein fragments shared >45% identity with other NarB and NirA proteins from Euryarchaeota and <38% identity with other nitrate reductases from Bacteria and Crenarchaeota . Furthermore, these clone sequences were clustered within the class Halobacteria with strong support values in both constructed dendrograms, confirming that desired PCR products were obtained. The metabolic capacity to assimilate nitrate by these haloarchaea seems to be important given that at pH 10 and higher, NH₄⁺ is mostly converted to toxic and volatile NH₃, and NO₃⁻ becomes the preferable N source.     

The alkaline,saline lakes of Uganda: a review

Most saline lakes in Uganda are alkaline and occur in closed basins associated with the Western Rift Valley. They are small shallow lakes exhibiting considerable temporal variation in volume and surface area. They have been categorized as maar lakes. Salinity in these lakes results from evaporative concentration of ions leached from their drainage basins. These lakes can be grouped into three broad categories: carbonate-chloride, sulphate-chloride, and chloride lakes according to the dominant anion(s). The relative amounts of ions in solution determines, in part, the limnochemical characteristics of the lakes. There is some evidence of thermal and chemical stratification in the deeper lakes. Records of the limnobiology in these lakes are scarce and not exhaustive.     

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern

Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development.     

宁夏不同地区盐碱化土壤细菌群落多样性分布特征及其影响因子

为了解宁夏不同地区盐碱化土壤细菌群落多样性的分布特征及其关键影响因子,选择贺兰县红星村、惠农县黄渠拐子、燕子墩、庙台、平罗县银星村、分水闸、侯家梁、西大滩为研究样点,采集宁夏地区8个典型盐碱化土壤样品,0—2 cm和2—25 cm土层,共48份。利用Illumina Hiseq高通量测序技术解析不同采样点土壤细菌群落结构的特征,同时分析了土壤理化因子与细菌群落结构的关系。试验结果表明:变形菌门、拟杆菌门和放线菌门为8个采样点土壤细菌群落的优势种类。其中,变形菌门占总量的24.69%—56.44%;γ-变形菌纲相对丰度在燕子墩土壤中显著高于其他样点(P<0.05)。0—2 cm土层,变形菌门相对丰度在燕子墩、红星村和分水闸这3个样点较高;拟杆菌门的相对丰度在分水闸样点土壤中最高;2—25 cm土层,变形菌门与表层土具有相同趋势;放线菌门的相对丰度在西大滩样点土壤中最高。在属水平,芽孢杆菌属是所有样点的优势属种。α多样性指数结果显示:燕子墩的土壤细菌群落多样性和丰富度都显著低于其他样点。土壤理化性质测定结果表明:在0—2 cm,全氮、有机碳、碱解氮、速效钾在黄渠拐子土壤中含量最高;含...     

Bacterial and fungal colonization of burn wounds

A prospective study of fungal and bacterial flora of burn wounds was carried out from February 2004 to February 2005 at the Burns Unit of Hospital Regional da Asa Norte, Brasília, Brazil. During the period of the study, 203 patients were treated at the Burns Unit. Wound swab cultures were assessed at weekly intervals for four weeks. Three hundred and fifty four sampling procedures (surface swabs) were performed from the burn wounds. The study revealed that bacterial colonization reached 86.6% within the first week. Although the gram-negative organisms, as a group, were more predominant, Staphylococcus aureus (28.4%) was the most prevalent organism in the first week. It was however surpassed by Pseudomonas aeruginosa form third week onwards. For S. aureus and P. aeruginosa vancomycin and polymyxin were found to be the most effective drugs. Most of the isolates showed high level resistance to antimicrobial agents. Fungi were found to colonize the burn wound late during the second week postburn, with a peak incidence during the third and fourth weeks. Species identification of fungi revealed that Candida tropicalis was the most predominant, followed by Candida parapsilosis. It is crucial for every burn institution to determine the specific pattern of burn wound microbial colonization, the time-related changes in the dominant flora, and the antimicrobial sensitivity profiles. This would enable early treatment of imminent septic episodes with proper empirical systemic antibiotics, without waiting for culture results, thus improving the overall infection-related morbidity and mortality.     

Bacterial colonization of particles: growth and interactions

Marine particles in the ocean are exposed to diverse bacterial communities, and colonization and growth of attached bacteria are important processes in the degradation and transformation of the particles. In an earlier study, we showed that the initial colonization of model particles by individual bacterial strains isolated from marine aggregates was a function of attachment and detachment. In the present study, we have investigated how this colonization process was further affected by growth and interspecific interactions among the bacteria. Long-term incubation experiments showed that growth dominated over attachment and detachment after a few hours in controlling the bacterial population density on agar particles. In the absence of grazing mortality, this growth led to an equilibrium population density consistent with the theoretical limit due to oxygen diffusion. Interspecific interaction experiments showed that the presence of some bacterial strains ("residents") on the agar particles either increased or decreased the colonization rate of other strains ("newcomers"). Comparison between an antibiotic-producing strain and its antibiotic-free mutant showed no inhibitory effect on the newcomers due to antibiotic production. On the contrary, hydrolytic activity of the antibiotic-producing strain appeared to benefit the newcomers and enhance their colonization rate. These results show that growth- and species-specific interactions have to be taken into account to adequately describe bacterial colonization of marine particles. Changes in colonization pattern due to such small-scale processes may have profound effects on the transformation and fluxes of particulate matter in the ocean.     

Bacterial colonization of domestic reverse-osmosis water filtration units

We have analyzed the bacterial content of water from the reservoirs of 300 reverse-osmosis units installed in households. The heterotrophic plate counts on R2A medium (20 and 35 degrees C) ranged from 0 to 10(7) colony forming units per millilitre (cfu/mL). Most reservoirs contained water with bacterial counts between 10(4) and 10(5) cfu/mL. The bacteria identified were Pseudomonas (not aeruginosa), Alcaligenes or Moraxella, Acinetobacter, Flavobacterium, and Chromobacterium. This report emphasizes the importance of bacterial colonization by heterotrophic bacteria in water reservoirs from domestic reverse-osmosis units.     

Mineralization of 14C-labelled maize in alkaline saline soils

The turnover of organic material determines the availability of plant nutrients in unfertilized soils, and this applies particularly to the alkaline saline soil of the former Lake Texcoco in Mexico. Uniformly labelled [¹⁴C] maize and its neutral detergent fibre (NDF) fraction, mainly containing cellulose and hemi-cellulose, were added to these soils to investigate dynamics of C and N and the importance of the NDF fraction. Soil with electrolytic conductivity (EC) of 1.2, 3.2, 24.6 and 32.7 dS m^–1 was incubated aerobically, while CO₂ and ¹⁴CO₂ production, and inorganic N dynamics (NH₄ ⁺, NO₂ ^–, NO₃ ^–) were monitored. The amount of ¹⁴C-labelled maize mineralized after 97 days was >500 mg C kg^–1 dry soil (D.S.) of the 1000 mg C kg^–1 D.S. added in soils with EC 24.6 dS m^–1, but only 257 mg C kg^–1 D.S. in soil with EC 32.7 dS m^–1. The decomposition of the NDF fraction showed a lag, greatest in the soil with the largest EC and the amount of ¹⁴C-labelled NDF fraction mineralized after 97 days was > 300 mg C kg^–1 D.S. in soils with EC 3.2 dS m^–1, but in the soil with EC 32.7 dS m^–1 it was only 118 mg C kg^–1D.S. Application of ¹⁴C-labelled maize and the NDF fraction induced a priming effect, most accentuated at the onset of the incubation. The ratio between the amount of CO₂ produced due to the priming effect and the ¹⁴CO₂ produced was 16-times larger when 250 mg maize-C kg^–1 D.S. was added and only 3-times when 2000 mg maize-C kg^–1 D.S. was added. Oxidation of NO₂ ^– occurred in soil with EC 32.7 dS m^–1 as witnessed by decreases in concentration of NO₂ ^– and increases in concentration of NO₃ ^–. It was found that EC affected the decomposition of maize, the NDF fraction and the priming effect. Decomposition of cellulose and oxidation of NO₂ ^– occurred in soil with EC 32.7 dS m^–1 although cellulolytic micro-organisms and autotrophic NO₂ ^– oxidizers could previously not be isolated from this soil.     

Bacterial 16S rDNA and alkaline phosphatase gene diversity in soil applied with composted aquatic plants

Limnology - The present study aimed to examine the effects of applying composted aquatic plants (CAP) on richness and composition of soil bacterial assemblages responsible for alkaline phosphatase...     

土壤因子对甘肃、宁夏和内蒙古盐碱土中AM真菌的影响

为探明甘肃、宁夏和内蒙古盐碱土中AM真菌多样性及其与土壤因子间的关系,2005年5月从甘肃、宁夏和内蒙古7个县(市)的盐碱土中采集主要植物的根围土壤样品,研究了AM真菌物种多样性.在分离的4属28种AM真菌中,球囊霉属(Glomus)20种,多孢囊霉属(Diversispora)2种,原囊霉属(Archaeospora)2种,无梗囊霉属(Acaulospora)4种.其中根内球囊霉(G.intraradices)和薄壁原囊霉(Ar.leptotihum)的分离频度最高.相关分析和通径分析(path analysis)结果表明,AM真菌种的丰度与土壤有机质和速效N含量呈显著负相关;Cl-、CO2-3、HCO-3、Na+、Ca2+、有机质、速效P和速效K直接影响AM真菌种的丰度,而SO2-4、K+、水溶性全盐、Mg2+、pH和速效N则间接影响AM真菌种的丰度;土壤有机质对AM真菌Shannon-Wiener多样性指数有显著直接负效应;Cl-、CO2-3、K+、Mg2+、有机质、速效P和速效K直接影响Shannon-Wiener多样性指数,而HCO-3、Na+、Ca2+、SO2-4、水溶性全盐、pH和速效N则间接影响Shannon-Wiener多样性指数.冗余度分析结果表明,AM真菌种的相对多度与土壤因子间有显著相关性.可见,甘肃、宁夏和内蒙古盐碱土中AM真菌种类丰富,其多样性与土壤养分状况、盐度以及离子含量有关.     

Bacterial colonization of patients treated with chronic hemodialysis]

The study was aimed at investigating the predispositions of the patients chronically treated with hemodialysis to nose and skin colonization with potentially pathogenic bacteria. The study involved 41 patients chronically hemodialysed and patients treated at the Department of Renal diseases or out-patient clinic (30 individuals). Smears from the nose and throat were taken from all patients and used for bacteriologic tests. In case of hemodialysed patients material for bacteriologic tests was additionally taken from the skin at the site of arterio-venous fistula and groin. It was found, that patients chronically treated with hemodialyses are more frequently colonized with enteric bacilli and coagulase-positive staphylococci that both hospitalized patients and those treated in out-patient clinic. No relationship between the presence of coagulase-positive staphylococci in the nose and throat and on the skin was seen despite such suggestions of other authors.     

Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico)

The diversity of the dissimilatory and respiratory nitrate-reducing communities was studied in two soils of the former lake Texcoco (Mexico). Genes encoding the membrane-bound nitrate reductase (narG) and the periplasmic nitrate reductase (napA) were used as functional markers. To investigate bacterial communities containing napA and narG in saline alkaline soils of the former lake Texcoco, libraries of the two sites were constructed (soil T3 with pH 11 and electrolytic conductivity in saturated extract (EC_SE) 160 dS m⁻¹ and soil T1 with pH 8.5 and EC_SE 0.8 dS m⁻¹). Phylogenetic analysis of napA sequences separated the clone families into two main groups: dependent or independent of NapB. Most of napA sequences from site T1 were grouped in the NapB-dependent clade, meanwhile most of the napA sequences from the extreme soil T3 were affiliated to the NapB-independent group. For both sites, partial narG sequences were associated with representatives of the Proteobacteria, Firmicutes and Actinobacteria phyla, but the proportions of the clones were different. Our results support the concept of a specific and complex nitrate-reducing community for each soil of the former lake Texcoco.     

Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations

Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the alpha-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11.     

Bacterial soil community in a Brazilian sugarcane field

The assessment of bacterial communities in soil gives insight into microbial behavior under prevailing environmental conditions. In this context, we assessed the composition of soil bacterial communities in a Brazilian sugarcane experimental field. The experimental design encompassed plots containing common sugarcane (variety SP80-1842) and its transgenic form (IMI-1 — imazapyr herbicide resistant). Plants were grown in such field plots in a completely randomized design with three treatments, which addressed the factors transgene and imazapyr herbicide application. Soil samples were taken at three developmental stages during plant growth and analyzed using 16S ribosomal RNA (rRNA)-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and clone libraries. PCR-DGGE fingerprints obtained for the total bacterial community and specific bacterial groups — Actinobacteria, Alphaproteobacteria and Betaproteobacteria — revealed that the structure of these assemblages did not differ over time and among treatments. Nevertheless, slight differences among 16S rRNA gene clone libraries constructed from each treatment could be observed at particular cut-off levels. Altogether, the libraries encompassed a total of eleven bacterial phyla and the candidate divisions TM7 and OP10. Clone sequences affiliated with the Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria were, in this order, most abundant. Accurate phylogenetic analyses were performed for the phyla Acidobacteria and Verrucomicrobia, revealing the structures of these groups, which are still poorly understood as to their importance for soil functioning and sustainability under agricultural practices.     

Micro-organic colonization of forest soil after burning

Summary and conclusions The results show that for some time, fire sites remain largely free of many of the micro-organisms that normally inhabit the soil and are then gradually colonized by species characteristic of burnt sites. Colonization was most pronounced at the margins due presumably to the invasion of the nutrient-rich soil of the fire site by mycellia from surrounding unburnt ground. The micro-organisms isolated from the centre of the burns during the early stages of succession, probably arise from spores brought in the wind and washed down by rain water.     

Growth and uptake of nitrogen by wheat and ryegrass in fumigated and irradiated soil

Summary Wheat and ryegrass were grown in pots containing soil that had either been irradiated, fumigated with methyl bromide, fumigated with formaldehyde, or left untreated. All pots received a basal dressing of potassium, phosphorus and magnesium; response to nitrogen was tested by applying either 0, 0.177 or 0.354 g nitrogen per pot. Irradiation increased the growth of wheat and ryegrass; uptake of nitrogen was also increased in both crops. The amount of fertilizer nitrogen equivalent to the nitrogen supplied by seeds and soil (the “N value”) can be calculated from the efficiency of uptake of fertilizer nitrogen and used to allow for the effect on crop growth of the nitrogen released by irradiated soil. With wheat the increase in growth can be attributed solely to the extra mineral nitrogen released by irradiated soil. However, ryegrass grew a little better than would have been expected if the only effect of irradiation was to increase the release of soil nitrogen. Fumigation with methyl bromide or formaldehyde increased the growth of wheat and ryegrass not given fertilizer nitrogen. However, fumigation with methyl bromide left ionic bromide in the soil, and this depressed the growth of wheat receiving fertilizer nitrogen. Formaldehyde also left residues; these influenced soil metabolism and sometimes depressed the growth of plants given fertilizer nitrogen.     

Bacterial colonization and biofilm development on minimally processed vegetables

Bacterial biofilms have been observed and reported on food and food-processing surfaces and can contribute to increased risks for product quality and food safety. The colonization of fruit and vegetables by pectynolitic bacteria like Pseudonomas fluorescens attributable to conditions such as soft rot, can also manifest as biofilms. A developed biofilm structure can provide a protective environment for pathogens such as Listeria monocytogenes reducing the effectiveness of sanitisers and other inhibitory agents. Understanding the colonization of bacteria on leaf surfaces is essential to the development of a better understanding of the leaf ecology of vegetable products. Studies of microbial colonization of leaf surfaces have been conducted using SEM and more recently using confocal microsocpy techniques. In the current study, a Leica TCS NT laser scanning confocal microscope was used to investigate biofilm formation using vital fluorescence staining on intact vegetable leaves. Reflection contrast and fluorescence three-dimensional imaging successfully delineated bacterial and biofilm morphology without disturbing the bacterial or leaf surface structure. The results demonstrate the presence and development of biofilm on the surface of lettuce. The biofilms appeared to originate on the cuticle in distinct micro-environments such as in the natural depression of the stomata, or in the intercellular junction. Bacteria also adhered to and developed biofilm colonies within an hour of contact and with clean stainless steel surfaces. Our study investigates the progression of biofilm formation from leaf colonization, and will assist in characterising the critical mechanisms of plant/host interaction and facilitate the development of improved preservation, sanitising and packaging strategies for minimally processed vegetable products.     

Bacterial functional redundancy along a soil reclamation gradient

A strategy to measure bacterial functional redundancy was developed and tested with soils collected along a soil reclamation gradient by determining the richness and diversity of bacterial groups capable of in situ growth on selected carbon substrates. Soil cores were collected from four sites along a transect from the Jamari tin mine site in the Jamari National Forest, Rondonia, RO, Brazil: denuded mine spoil, soil from below the canopy of invading pioneer trees, revegetated soil under new growth on the forest edge, and the forest floor of an adjacent preserved forest. Bacterial population responses were analyzed by amending these soil samples with individual carbon substrates in the presence of bromodeoxyuridine (BrdU). BrdU-labeled DNA was then subjected to a 16S-23S rRNA intergenic analysis to depict the actively growing bacteria from each site. The number and diversity of bacterial groups responding to four carbon substrates (L-serine, L-threonine, sodium citrate, and alpha-lactose hydrate) increased along the reclamation-vegetation gradient such that the preserved forest soil samples contained the highest functional redundancy for each substrate. These data suggest that bacterial functional redundancy increases in relation to the regrowth of plant communities and may therefore represent an important aspect of the restoration of soil biological functionality to reclaimed mine spoils. They also suggest that bacterial functional redundancy may be a useful indicator of soil quality and ecosystem functioning.     

Bacterial interference with skin colonization in germfree hairless mice

Bacterial colonization of the digestive tract and the skin was studied over a 3-week period in a group of 10 germfree HRS mice using Staphylococcus epidermidis, Staphylococcus aureus, and Pseudomonas aeruginosa. Sequential utilization of two strains allowed us to carry out six assays and to show the presence of interference phenomena during colonization of the skin. When P. aeruginosa was given after challenge with S. aureus or S. epidermidis, it did not colonize the skin. If the first challenge was done with P. aeruginosa, this bacteria was eliminated within 10 days by S. aureus and S. epidermidis on the skin, but it succeeded in colonizing the digestive tract. When the first challenge was done with S. aureus, colonization of the skin and the digestive tract with S. epidermidis was prevented, whereas these two species were found in association when S. aureus was given in second place. None of the in vitro assays (mixed culture, bacteriocin production, adherence inhibition, antimicrobial activity) could explain the in vivo observations.     

微生物肥料在盐碱土壤中的应用展望

随着土地资源日益短缺及人们对生态环境的关注,以天然土壤微生物为主要成分的微生物肥料应用在盐碱农业中越来越受到重视。本文综述了国内外微生物肥料的发展历史和现状,微生物肥料对盐碱土壤产生的影响,帮助植物抵抗盐胁迫的机制,以及对盐碱土壤中微生物群落产生的影响;本文也提出了两种能够有效保藏菌种的固定化方法,这两类方法能有效地解决菌种易失活问题且延长其在土壤中的作用时间;最后提出了目前微生物肥料作用于盐碱地存在的问题与展望,旨在为缓解土地资源、提高农业安全生产做出贡献。