Changes in methane oxidation activity and methanotrophic community composition in saline alkaline soils

The soil of the former Lake Texcoco is a saline alkaline environment where anthropogenic drainage in some areas has reduced salt content and pH. Potential methane (CH₄) consumption rates were measured in three soils of the former Lake Texcoco with different electrolytic conductivity (EC) and pH, i.e. Tex-S1 a >18 years drained soil (EC 0.7 dS m^?1, pH 8.5), Tex-S2 drained for ~10 years (EC 9.0 dS m^?1, pH 10.3) and the undrained Tex-S3 (EC 84.8 dS m^?1, pH 10.3). An arable soil from Alcholoya (EC 0.7 dS m^?1, pH 6.7), located nearby Lake Texcoco was used as control. Methane oxidation in the soil Tex-S1 (lowest EC and pH) was similar to that in the arable soil from Alcholoya (32.5 and 34.7 mg CH₄ kg^?1 dry soil day^?1, respectively). Meanwhile, in soils Tex-S2 and Tex-S3, the potential CH₄ oxidation rates were only 15.0 and 12.8 mg CH₄ kg^?1 dry soil day^?1, respectively. Differences in CH₄ oxidation were also related to changes in the methane-oxidizing communities in these soils. Sequence analysis of pmoA gene showed that soils differed in the identity and number of methanotrophic phylotypes. The Alcholoya soil and Tex-S1 contained phylotypes grouped within the upland soil cluster gamma and the Jasper Ridge, California JR-2 clade. In soil Tex-S3, a phylotype related to Methylomicrobium alcaliphilum was detected.     

Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium

Poplar trees (Populus spp.) are often used in bioremediation strategies because of their ability to phytoextract potential toxic ions, e.g., selenium (Se) from poor quality soils. Soil microorganisms may play a vital role in sustaining health of soil and/or tolerance of these trees grown in poor quality soils by contributing to nutrient cycling, soil structure, overall soil quality, and plant survival. The effect of naturally occurring salts boron (B) and Se on soil microbial community composition associated with poplar trees is not known for bioremediation strategies. In this study, three Populus clones 13–366, 345–1, and 347–14 were grown in spring 2006 under highly saline, B, and Se clay-like soils in the west side of the San Joaquin Valley (SJV) of CA, as well as in non-saline sandy loam soils located in the east side of the SJV. After 7 years of growing in the respective soils of different qualities, soil samples were collected from poplar clones grown in saline and non-saline soils to examine and compare soil quality effects on soil microbial community biomass and composition. The phospholipid fatty acid (PLFA) analysis was used to characterize microbial community composition in soils from trees grown at both locations. This study showed that microbial biomass and the amount and proportion of arbuscular mycorrhizal fungal (AMF) community were lower in all three poplar clones grown in saline soil compared to non-saline soil. Amounts of Gram + bacterial and actinomycetes PLFAs were significantly lower in poplar clone 13–366 grown in saline soil compared to non-saline soil; however, they did not differ significantly in poplar clones 347–14 and 345–1. Additionally, amounts of saprophytic fungal, Gram ? bacterial and eukaryotic PLFA remained similar at saline and non-saline sites under poplar clones 347–14, 345–1, and 13–366. Therefore, this study suggested that salinity and B do have an impact on microbial biomass and AMF; however, these poplar clones still recycled sufficient amount of nutrients to support and protect saprophytic fungal and bacterial communities from the effects of poor quality soils.     

Salinity tolerance and ecological aspects of some microfungi from saline and non-saline soils in Wyoming

The salt tolerance ofActinomucor harzii andPenicillium lilacinum both garden soil dominants and twoCephalosporium species from saline soils in Wyoming was investigated. BothCephalosporium species exhibited growth maxima, in culture, at salt concentrations approximating those of the habitat from which they were obtained.P. lilacinum exhibited an ability to adjust, with time, to high MgSO₄ concentrations and is considered salt-tolerant.A. harzii was consistently salt-sensitive. The ecological significance of the investigation is discussed.     

Microbial community composition in soils of Northern Victoria Land, Antarctica

Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme systems are highly diverse with patchy distributions. Investigating the physical and biological controls over the distribution and activity of microbial biodiversity in Victoria Land is essential to understanding ecological functioning in this region. Currently, little information on the distribution, structure and activity of soil communities anywhere in Victoria Land are available, and their sensitivity to potential climate change remains largely unknown. We investigated soil microbial communities from low- and high-productivity habitats in an isolated Antarctic location to determine how the soil environment impacts microbial community composition and structure. The microbial communities in Luther Vale, Northern Victoria Land were analysed using bacterial 16S rRNA gene clone libraries and were related to soil geochemical parameters and classical morphological analysis of soil metazoan invertebrate communities. A total of 323 16S rRNA gene sequences analysed from four soils spanning a productivity gradient indicated a high diversity (Shannon-Weaver values > 3) of phylotypes within the clone libraries and distinct differences in community structure between the two soil productivity habitats linked to water and nutrient availability. In particular, members of the Deinococcus/Thermus lineage were found exclusively in the drier, low-productivity soils, while Gammaproteobacteria of the genus Xanthomonas were found exclusively in high-productivity soils. However, rarefaction curves indicated that these microbial habitats remain under-sampled. Our results add to the recent literature suggesting that there is a higher biodiversity within Antarctic soils than previously expected.     

Microbial community composition and function beneath temperate trees exposed to elevated atmospheric carbon dioxide and ozone

We hypothesized that changes in plant growth resulting from atmospheric CO₂ and O₃ enrichment would alter the flow of C through soil food webs and that this effect would vary with tree species. To test this idea, we traced the course of C through the soil microbial community using soils from the free-air CO₂ and O₃ enrichment site in Rhinelander, Wisconsin. We added either ¹³C-labeled cellobiose or ¹³C-labeled N-acetylglucosamine to soils collected beneath ecologically distinct temperate trees exposed for 3 years to factorial CO₂ (ambient and 200 µl l^-1 above ambient) and O₃ (ambient and 20 µl l^-1 above ambient) treatments. For both labeled substrates, recovery of ¹³C in microbial respiration increased beneath plants grown under elevated CO₂ by 29% compared to ambient; elevated O₃ eliminated this effect. Production of ¹³C-CO₂ from soils beneath aspen (Populus tremuloides Michx.) and aspen-birch (Betula papyrifera Marsh.) was greater than that beneath aspen-maple (Acer saccharum Marsh.). Phospholipid fatty acid analyses (¹³C-PLFAs) indicated that the microbial community beneath plants exposed to elevated CO₂ metabolized more ¹³C-cellobiose, compared to the microbial community beneath plants exposed to the ambient condition. Recovery of ¹³C in PLFAs was an order of magnitude greater for N-acetylglucosamine-amended soil compared to cellobiose-amended soil, indicating that substrate type influenced microbial metabolism and soil C cycling. We found that elevated CO₂ increased fungal activity and microbial metabolism of cellobiose, and that microbial processes under early-successional aspen and birch species were more strongly affected by CO₂ and O₃ enrichment than those under late-successional maple.     

Phosphorus status of some saline and non-saline hydromorphic soils of the Niger Delta of Nigeria

Summary The phosphorus status of some mangrove and fresh-water hydromorphic soils of the Nigerian Niger Delta was evaluated by determining the relative abundance of various P forms and the P-sorption capacity indices. Total P was high in all soils ranging from 352 to 2055 mg/kg, with a mean of 1011 mg/kg. The saline mangrove-swamp soils had generally higher values than the fresh-water soils. Organic P formed about 34% of total P. The relative abundance of the inorganic P forms was in decreasing order, active P, occluded P and residual P. The relative distribution of active P followed the decreasing order, Fe–P, Al–P and Ca–P.The adsorption capacity was generally low in all soils. The amount of P sorbed from the addition of 150 mg/100g of soil ranged from zero to 13 mg/100g, giving an average of about 7% of added P sorbed.The abundance of active P and low content of occluded P were attributed to the poorly drained and unweathered nature of the soils. The low P adsorption suggests little capacity of the soils to fix P. The relatively high content of active P and the low P sorption capacity generally indicate high availability of P to plant in these soils.     

Calcium requirement of wheat in saline and non-saline conditions

Supplemental calcium (Ca²⁺) is used in hydroponic studies on salinity to lessen the potential for Ca²⁺ deficiency. However, the Ca²⁺ concentration and the sodium (Na⁺): Ca²⁺ ratio used vary considerably. The implications of using a wide range of Na⁺: Ca²⁺ ratios for studies of salinity tolerance in wheat are not known. Also, despite the risk of development of Ca²⁺ deficiency under salinity stress, there are few reliable reports on the critical level of Ca²⁺ which can be used to diagnose Ca²⁺ deficiency in wheat. Two experiments were conducted to examine Ca²⁺ requirements of wheat under saline and non-saline conditions and to derive a critical level for Ca²⁺. Four bread wheat genotypes (Triticum aestivum L.) and a durum wheat genotype [Triticum turgidum subsp. durum) (Desf.) Husn.] with known differences in salinity tolerance were grown at 100 mM NaCl for four weeks with varying levels of external Ca²⁺ which resulted in Na⁺:Ca²⁺ ratios of 30, 20, 15, 5 and 2. The critical Ca²⁺ concentration was defined in a second experiment by growing the same wheat genotypes at seven levels of Ca²⁺ (0.05, 0.1, 0.2, 0.5, 1, 2 and 10 mM) under non-saline conditions. When grown at 100 mM NaCl salinity tolerance was greatest when the Na⁺:Ca²⁺ ratio ranged from 5 to 15. Growing plants at lower or higher Na⁺:Ca²⁺ ratios induced nutrient imbalances and additional osmotic stress which reduced the growth of plants. Transient Ca²⁺ deficiency occurred at high Na⁺:Ca²⁺ ratios and low Mg²⁺ occurred at the lowest Na⁺:Ca²⁺ ratio. Adding NaCl raised the tissue Na⁺ concentration and reduced the Ca²⁺ concentration and the most appropriate Na⁺:Ca²⁺ ratio in the solution was that which resulted in tissue Ca²⁺ concentrations similar to those of non-salinised plants. The critical level of Ca²⁺ in the youngest fully emerged leaf blades was 15–23 mmol kg^-1 DW (600–900 mg kg^-1 DW).     

Differences in chemical composition ofAlysicarpus vaginalis (L.) DC. growing in saline and non-saline habitats

InAlysicarpus vaginalis (L.) DC. nitrogen, ascorbic acid, proline and epicuticular wax (ECW) contents were higher in the plants growing in the coastal region whereas the protein, soluble sugars and starch contents were lower. The higher contents of proline, nitrogen and ascorbic acid recorded in the plants of the saline habitat are a physiological adaptation to overcome the salt stress. The higher ECW content in the plants of the saline habitat specially in the summer months seems to be an adaptation in these plants to survive in the saline habitat. Communicated by Z. ŠESTáK     

Diversity,community composition,and bioactivity of cultivable fungal endophytes in saline and dry soils in deserts

Fungal endophyte communities are poorly investigated in extreme habitats such as deserts. We used cultivation and Sanger sequencing to investigate the effects of environmental variables on the endophytic fungal communities of eight Iranian desert plants. Host species was the main factor shaping the endophyte composition, while soil type additionally affected endophytes of above- and below-ground organs. Redundancy analysis showed that soil pH and electric conductivity determine fungal endophyte communities in plants in dry and saline soils. In a follow-up experiment, we showed that these endophytes could be used in crop production under salinity/drought stress and as biocontrol agents. Although compared to other ecosystems, the endophytic fungi associated with the studied Iranian desert plants are of low diversity, our results suggest that they probably play an essential role in the survival of their hosts. Further investigation is necessary to evaluate the potential benefits and applicability of such endophytes in agricultural practices in drylands.     

Effects of salinity on microbial tolerance to drying and rewetting

Soil salinity and fluctuations in soil matric potential are stressors for soil microorganisms which, in turn, may affect soil organic matter turnover. In response to salinity and low soil water content, many microorganisms accumulate osmolytes. Therefore, it is conceivable that microorganisms in saline soils are more tolerant to drying and rewetting (DRW) stress than those in non-saline soils. An experiment was carried out with three different salinity levels: electrical conductivity (EC_1:5) 0, 2 and 4 dS m^?1 (EC0, EC2, EC4), and two water treatments: a constantly moist control or two DRW cycles. Respiration as an indicator of microbial activity was measured throughout the 59 days of incubation. At the end of the second dry period (day 35) and at the end of the following moist incubation (day 59), microbial biomass and microbial community structure were determined by phospholipid fatty acid (PLFA) analysis. Increasing salinity decreased microbial activity but did not affect its resistance to DRW. On day 59, cumulative respiration decreased in the order EC0 > EC2 > EC4 with no differences between water treatments. Fungal biomass was negatively affected by salinity at the end of the experiment, while bacterial biomass was unaffected. Microbial community structure in moist treatments differed between salinity levels, with EC4 influencing microbial community structure earlier than EC2. The resistance of microbial communities to DRW stress was salt level dependent; only beyond a critical salinity level adaptation to salt stress was able to reduce the impact of water stress on microbial community structure.     

Effects of sieving, drying and rewetting upon soil bacterial community structure and respiration rates

Soil microcosm studies often require some form of soil homogenisation, such as sieving, to provide a representative sample. Frequently, soils are also homogenised following drying and are then rewetted, yet little research has been done to understand how these methods impact upon microbial communities. Here we compared the molecular diversity and functional responses of intact cores from a Scottish grassland soil with homogenised samples prepared by drying, sieving and rewetting or freshly sieving wet soils. Results showed that there was no significant difference in total soil CO₂-C efflux between the freshly sieved and intact core treatments, however, respiration was significantly higher in the dried and rewetted microcosms. Molecular fingerprinting (T-RFLP) of bacterial communities at two different time-points showed that both homogenisation methods significantly altered bacterial community structure with the largest differences being observed after drying and rewetting. Assessments of responsive taxa in each treatment showed that intact cores were dominated by Acidobacterial peaks whereas an increased relative abundance of Alphaproteobacterial terminal restriction fragments were apparent in both homogenised treatments. However, the shift in community structure was not as large in the freshly sieved soil. Our findings suggest that if soil homogenisation must be performed, then fresh sieving of wet soil is preferable to drying and rewetting in approximating the bacterial diversity and functioning of intact cores.     

固沙植被区土壤呼吸对反复干湿交替的响应

由降水的不连续性引起的土壤干湿交替是荒漠生态系统土壤呼吸的重要影响因子。在恒温培养条件下,研究了固沙植被区土壤呼吸对不同降雨量(5、10、20 mm)条件下以10 d为降水周期的多重干湿交替过程的响应,结果表明:3个降雨量条件下的多重干湿交替过程中,土壤呼吸速率均在降雨后迅速增大,并在降雨0.5 h后达到最大值,尔后,随着土壤含水量的下降而逐渐减小并恢复到降雨前水平。随着干湿交替过程的依次进行,最大和平均土壤呼吸速率及累积碳释放量均呈现出逐渐减小的趋势。3个干湿循环周期平均呼吸速率和土壤碳释放量均随着降雨量的增加逐渐增大,土壤呼吸速率峰值表现为第1个干湿循环周期土壤呼吸速率峰值随着降雨量的增加而增大,而第2、3个周期各降雨处理下的土壤呼吸速率峰值显示出随着降雨前期土壤含水量的增加而减小的趋势。说明干湿交替过程对土壤呼吸具有显著的激发作用,且干湿交替程度(即降雨前后土壤含水量的变化)以及土壤前期所经历的干湿交替过程是影响荒漠生态系统土壤呼吸对干湿交替响应的重要因素。     

Microbial characteristics of sandy soils exposed to diazinon under laboratory conditions

Changes in microbiological characteristics in response to diazinon, applied at three different dosages of 7, 35 and 700 mg kg^?1 soil, were studied in pots filled with sandy soils of different texture. The insecticide dosages corresponded to the maximum predicted environmental concentration (PEC) in field conditions and five or hundred times this rate, respectively. To ascertain these changes, activities of selected soil enzymes, numbers of some microbial populations and bacterial community structure (r/K-strategists) were determined. Acid phosphatase activity and concentrations of ammonium ions either increased or were unaffected by the diazinon dosages. In contrast, nitrate ions, alkaline phosphatase, urease and especially dehydrogenase activities decreased in both soils treated with the higher dosages of the insecticide. The diazinon treatments increased the numbers of culturable bacteria and fungi; however, N-fixing bacteria and nitrifiers (but not denitrifiers) were decreased in both soils. When the high concentration of diazinon (100-times PEC) was added to the loamy sand soil (LS), simulating an undiluted chemical spill, the bacterial community structure shifted towards domination of K-strategists over time. However, r-strategists dominated in the community exposed to the same dosage of the insecticide in the sandy loam soil (SL). Generally, SL soil characteristics were more suitable for microbial activity and growth than those of LS soil were. The results indicate that except a situation of undiluted spill diazinon seems to be a non-hazardous chemical for the culturable soil microorganisms when applied at recommended concentrations.     

干湿交替下草地生态系统土壤呼吸变化的微生物响应机制研究进展

草地是陆地生态系统中最重要、分布最广的生态系统类型之一,对全球碳循环和气候调节有着重要的作用和效应.我国拥有极为丰富的草地资源,是巨大的陆地碳储存库,也是全球碳循环重要组成部分.干湿交替是土壤中普遍发生的自然现象,这种现象的发生可能会加速土壤的碳矿化过程、激增土壤呼吸以及影响微生物的活性和群落结构等.在全球变化日趋显著的背景下,降雨量、降雨强度以及降雨频率的变化将会加速土壤干湿交替进程,进而带来微生物活性、群落结构以及土壤呼吸的变化,并对全球碳循环过程产生重要影响.本文综述了近十年来国内外的相关文献,对干湿交替条件下,土壤释放CO₂消耗碳源、土壤呼吸随时间的动态变化趋势以及土壤呼吸与微生物量、微生物活性和微生物群落结构之间的关系进行了分析和总结,以期为更好地理解干湿交替过程中草地生态系统土壤呼吸的微生物学响应机制,更准确地预测和评估未来的全球陆地生态系统的碳收支与气候变化提供一定的理论基础.     

Microbial community in black rust exposed to hot ridge flank crustal fluids

During Integrated Ocean Drilling Program Expedition 301, we obtained a sample of black rust from a circulation obviation retrofit kit (CORK) observatory at a borehole on the eastern flank of Juan de Fuca Ridge. Due to overpressure, the CORK had failed to seal the borehole. Hot fluids from oceanic crust had discharged to the overlying bottom seawater and resulted in the formation of black rust analogous to a hydrothermal chimney deposit. Both culture-dependent and culture-independent analyses indicated that the black-rust-associated community differed from communities reported from other microbial habitats, including hydrothermal vents at seafloor spreading centers, while it shared phylotypes with communities previously detected in crustal fluids from the same borehole. The most frequently retrieved sequences of bacterial and archaeal 16S rRNA genes were related to the genera Ammonifex and Methanothermococcus, respectively. Most phylotypes, including phylotypes previously detected in crustal fluids, were isolated in pure culture, and their metabolic traits were determined. Quantification of the dissimilatory sulfite reductase (dsrAB) genes, together with stable sulfur isotopic and electron microscopic analyses, strongly suggested the prevalence of sulfate reduction, potentially by the Ammonifex group of bacteria. Stable carbon isotopic analyses suggested that the bulk of the microbial community was trophically reliant upon photosynthesis-derived organic matter. This report provides important insights into the phylogenetic, physiological, and trophic characteristics of subseafloor microbial ecosystems in warm ridge flank crusts.     

Microbial activity in soils following steam treatment

Steam enhanced extraction (SEE) is an aquifer remediation technique that can be effective at removing the bulk of non-aqueous phase liquid (NAPL) contamination from the subsurface, particularly highly volatile contaminants. However, low volatility compounds such as polynuclear aromatic hydrocarbons (PAHs) are less efficientlyremoved by this process. This research evaluated the effects of steam injection on soilmicrobial activity, community structure, and the potential for biodegradation of contaminants following steam treatment. Three different soils were evaluated: alaboratory-prepared microbially-enriched soil, soil from a creosote contaminated fieldsite, and soil from a chlorinated solvent and waste oil contaminated field site. Results from field-scale steaming are also presented. Microbial activity before and after steam treatment was evaluated using direct epifluorescent microscopy (DEM) using the respiratory activity dye 5-cyano-2,3, ditolyl tetrazolium chloride (CTC) in conjunction with the fluorochrome 5-(4,6-dichlorotriazinyl) aminofluorescein (DTAF) to yield a quantitative assessment of active and total microbial numbers. DEM results indicate that steamed soils that were analyzed while still hot exhibited microbial activity levels that were below detection. However, soil samples that were slowly cooled, more closely reflecting the conditions of applied SEE, exhibited microbial activity levels that were comparable to presteamed soils. Samples from a field-site where steam was applied continuously for 6 weeks also showed high levels of microbial activity following cooling. The metabolic capabilities of the steamed communities were investigated by measuring cell growth in enrichment cultures on various substrates. These studies provided evidence that organisms capable of biodegradation were among the mesophilic populations that survived steam treatment. Fluorescent in situ hybridization (FISH) analysis of the soils with domain-level rRNA probes suggest that both Archaea and Bacteria survived steam exposure.     

盐碱旱地转基因抗虫棉田昆虫群落多样性

棉花是耐干旱和耐盐碱的经济作物。随着土壤的盐碱化和干旱化, 在人口数量和植棉成本剧增的背景下, 我国黄河流域和长江流域棉花种植面积锐减, 棉花种植被迫向滨海盐碱地和内陆及西北干旱地区转移。本文于2013年和2014年在山东东营滨海盐碱地和河北枣强半干旱轻度盐碱地以非转基因棉(‘中棉所49’)为对照, 以转Bt基因棉(‘中棉所79’)为试验材料, 分别作施农药和不施农药处理, 于每年5月初到9月中旬, 调查取样点棉株及地面上害虫及其天敌的种类和数量, 并分析不同施药处理下转基因和非转基因棉田昆虫群落的生物多样性参数差异。结果表明, 施药和不施药转Bt基因棉田昆虫群落和害虫亚群落昆虫的个体总数均低于非转基因棉田, 其中昆虫群落和害虫亚群落个体数在二者之间差异显著; 转Bt基因棉田昆虫群落和害虫亚群落昆虫的多样性指数和均匀度指数均高于非转基因棉田, 而优势集中性指数均低于非转基因棉田, 但差异均不显著。施药条件下两种棉田的昆虫群落和害虫亚群落昆虫个体总数、多样性指数和均匀度指数均低于不施药棉田, 优势集中性指数均高于不施药棉田, 但转基因棉田和非转基因棉田之间无显著差异。表明转基因抗虫棉在盐碱旱地对棉田靶标害虫具有较好的控制作用, 棉田昆虫群落稳定性较高, 昆虫群落对外界的入侵和干扰缓冲能力强, 而化学农药的使用对昆虫群落杀伤力较大, 容易导致某种昆虫的抗性产生和昆虫群落的不稳定, 但比非盐碱旱地棉田昆虫群落生物多样性低, 棉田生态系统更简单。     

Microbial community composition and function in wastewater treatment plants

Biological wastewater treatment has been applied for more than a century to ameliorate anthropogenic damage to the environment. But only during the last decade the use of molecular tools allowed to accurately determine the composition, and dynamics of activated sludge and biofilm microbial communities. Novel, in many cases yet not cultured bacteria were identified to be responsible for filamentous bulking and foaming as well as phosphorus and nitrogen removal in these systems. Now, methods are developed to infer the in situ physiology of these bacteria. Here we provide an overview of what is currently known about the identity and physiology of some of the microbial key players in activated sludge and biofilm systems. This revised version was published online in August 2006 with corrections to the Cover Date.