The nitrite-oxidizing community in activated sludge from a municipal wastewater treatment plant determined by fatty acid methyl ester-stable isotope probing

Metabolically-active autotrophic nitrite oxidizers from activated sludge were labeled with ¹³C-bicarbonate under exposure to different temperatures and nitrite concentrations. The labeled samples were characterized by FAME-SIP (fatty acid methyl ester-stable isotope probing). The compound cis-11-palmitoleic acid, which is the major lipid of the most abundant nitrite oxidizer in activated sludge, Candidatus Nitrospira defluvii, showed ¹³C-incorporation in all samples exposed to 3 mM nitrite. Subsequently, the lipid cis-7-palmitoleic acid was labeled, and it indicated the activity of a nitrite oxidizer that was different from the known Nitrospira taxa in activated sludge. The highest incorporation of cis-7-palmitoleic acid label was found after incubation with a nitrite concentration of 0.3 mM at 17 and 22 °C. While activity of Nitrobacter populations could not be detected by the FAME-SIP approach, an unknown nitrite oxidizer with the major lipid cis-9 isomer of palmitoleic acid exhibited ¹³C-incorporation at 28 °C with 30 mM nitrite. These results indicated flexibility of nitrite-oxidizing guilds in a complex community responding to different conditions. Labeled lipids so far not described for activated sludge-associated nitrifiers indicated the presence of unknown nitrite oxidizers in this habitat. The FAME-SIP-based information can be used to define appropriate conditions for the enrichment of nitrite-oxidizing guilds from complex samples.     

Impacts of 3 years of elevated atmospheric CO2 on rhizosphere carbon flow and microbial community dynamics

Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO₂ emissions. Short‐term atmospheric elevated CO₂ exposure has been shown to create major shifts in C flow routes and diversity of the active soil‐borne microbial community. Long‐term increases in CO₂ have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO₂ exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO₂ concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by ¹³C pulse‐chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA‐stable isotope probing (RNA‐SIP), in combination with real‐time PCR and PCR‐DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO₂ was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO₂ caused a continuous increase in the ¹³C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO₂ conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.     

岷江干旱河谷优势灌丛对土壤微生物群落组成的影响

通过调查岷江干旱河谷两河口、飞虹、撮箕和牟托4个样地优势灌丛及其灌丛间空地的表土土壤物理化学性质和微生物群落组成,探讨植物灌丛群落对土壤微生物群落组成的影响。研究发现不同灌丛种类对土壤微生物群落组成以及土壤物理化学性质并没有显著影响,而同一样地灌丛与空地间的差异却较为显著。灌丛下比空地土壤中具有更高的有机质、养分含量,更高的土壤含水量和更低的容重,而灌丛下相对富集的养分资源是造成灌丛与空地间微生物群落组成差异的主要原因。不同样地影响微生物群落的主要因子存在一定差异,但与氮相关的因子(总氮、有效氮、碳/氮比)对土壤微生物群落着非常重要的影响,特别是对土壤微生物群落总生物量和细菌类群(革兰氏阳性菌、革兰氏阴性菌、细菌等)。虽然不同灌丛和空地下土壤中细菌群落都没有显著地变化,但真菌和菌根真菌却明显的在灌丛下富集。在飞虹和牟托样地,总磷和碳/磷比与真菌类群,主要指真菌和菌根真菌,表现出显著正相关性,这或许反映了真菌类群对于该区域磷循环的重要作用。研究结果揭示了灌丛植被在干旱河谷地区地下生态系统中的重要作用,以及氮、磷这两种养分元素对土壤微生物群落的重要影响。同时,未来对于干旱河谷地区植物-土壤关系的研究应该关注真菌和菌根真菌类群的作用。     

若尔盖高寒湿地干湿土壤条件下微生物群落结构特征

土壤水分含量的空间异质性是引起湿地生态系统结构和功能空间变异的关键因素。目前有关低纬度高寒湿地土壤水分对微生物群落结构影响的研究较少。于2007年4月(冷季)和8月(暖季)采集若尔盖高寒湿地常年淹水和无淹水两种水分条件的土壤样品,利用磷脂脂肪酸方法分析其微生物群落结构。结果表明,土壤微生物总生物量、细菌生物量、革兰氏阳性细菌及革兰氏阴性细菌生物量均表现为常年淹水土壤高于无淹水土壤,且4月份高于8月份;与土壤通气量关系密切的真菌、放线菌,其生物量表现为无淹水土壤显著高于常年淹水土壤;反映群落组成的真菌:细菌磷脂脂肪酸比值也表现为无淹水土壤显著高于常年淹水土壤。磷脂脂肪酸的主成分分析表明,水分条件不同的两种土壤中微生物群落结构显著不同,季节变化并未引起土壤微生物群落结构的改变。     

Microbial Community Composition Near Depleted Uranium Impact Points

Military training activities can result in the deposition of depleted uranium (DU) into surface soils. Mechanisms of introduction include the generation of dust from firing and impact as well as the eventual corrosion of projectile fragments and unexploded ordnance. Microorganisms in surface soils have the potential to affect the transport of DU by direct binding of the metal to the cell surface, by altering near field soil chemistry that affects metal solubility, and by microbially influenced corrosion. We investigated the response (in terms of community composition) of a native soil microbiota to the presence of DU in an arid environment. Bacteria in soils outside of the test area were challenged in dilute media with “yellow cake” or U ₃ O ₈ . At concentrations of 200 to 20,000 mg L^{? 1} only species of Bacillus were identified. In situ characterizations (by PLFA analysis) of exposed site soils showed an enrichment in sulfate reducing bacterial (i17:1w7c up 39%) and Bacillus species (a15:0 up 35%) biomarkers. Three types of microbial communities were defined (as PLFA profiles) using exploratory statistics and related to three different levels of DU exposure. The community types were then statistically corresponded to site soil chemistry. Observed differences in site soil chemistry were attributed to munitions firing since enrichments (unexposed to exposed) were observed in the minerals magnesium (increase of ～ 18 mg kg^?1 ), potassium (increase of ～ 46 mg kg^?1 ) and sulfur (increase of ～ 12 mg kg^?1 ), all constituents of munitions residues. Increased concentrations of these minerals corresponded with a community type that was associated with an area of extensive DU round use.     

Microbial communities and activities in alpine and subalpine soils

Soil samples were collected along two slopes (south and north) at subalpine (1500–1900 m, under closed vegetation, up to the forest line) and alpine altitudes (2300–2530, under scattered vegetation, above the forest line) in the Grossglockner mountain area (Austrian central Alps). Soils were analyzed for a number of properties, including physical and chemical soil properties, microbial activity and microbial communities that were investigated using culture-dependent (viable heterotrophic bacteria) and culture-independent methods (phospholipid fatty acid analysis, FISH). Alpine soils were characterized by significantly ( P <0.01) colder climate conditions, i.e. lower mean annual air and soil temperatures, more frost and ice days and higher precipitation, compared with subalpine soils. Microbial activity (soil dehydrogenase activity) decreased with altitude; however, dehydrogenase activity was better adapted to cold in alpine soils compared with subalpine soils, as shown by the lower apparent optimum temperature for activity (30 vs. 37 °C) and the significantly ( P <0.01–0.001) higher relative activity in the low-temperature range. With increasing altitude, i.e. in alpine soils, a significant ( P <0.05–0.01) increase in the relative amount of culturable psychrophilic heterotrophic bacteria, in the relative amount of the fungal population and in the relative amount of Gram-negative bacteria was found, which indicates shifts in microbial community composition with altitude.     

High turnover of fungal hyphae in incubation experiments

Soil biological studies are often conducted on sieved soils without the presence of plants. However, soil fungi build delicate mycelial networks, often symbiotically associated with plant roots (mycorrhizal fungi). We hypothesized that as a result of sieving and incubating without plants, the total fungal biomass decreases. To test this, we conducted three incubation experiments. We expected total and arbuscular mycorrhizal (AM) fungal biomass to be higher in less fertilized soils than in fertilized soils, and thus to decrease more during incubation. Indeed, we found that fungal biomass decreased rapidly in the less fertilized soils. A shift towards thicker hyphae occurred, and the fraction of septate hyphae increased. However, analyses of phospholipid fatty acids (PLFAs) and neutral lipid fatty acids could not clarify which fungal groups were decreasing. We propose that in our soils, there was a fraction of fungal biomass that was sensitive to fertilization and disturbance (sieving, followed by incubation without plants) with a very high turnover (possibly composed of fine hyphae of AM and saprotrophic fungi), and a fraction that was much less vulnerable with a low turnover (composed of saprotrophic fungi and runner hyphae of AMF). Furthermore, PLFAs might not be as sensitive in detecting changes in fungal biomass as previously thought.     

Plant Recruitment and Soil Microbial Characteristics of Rehabilitation Seedings Following Wildfire in Northern Utah

One goal of post‐fire native species seeding is to increase plant community resistance to exotic weed invasions, yet few studies address the impacts of seeding on exotic annual establishment and persistence. In 2010 and 2011, we investigated the influence of seedings on exotic annuals and the underlying microbial communities. The wildfire site in northern Utah was formerly dominated by Artemisia tridentata ssp. wyomingensis, but burned in September 2008. Experimental seeding treatments were installed in November 2008 to examine strategies for establishing native species using two drills, hand broadcasts and different timing of seed applications (resulting in 13 seeding treatments). We collected aboveground biomass of invasive annuals (Halogeton glomeratus, Salsola kali, and Bromus tectorum), other volunteer plants from the extant seed bank, and seeded species from all treatments in the second and third years after fire. We sampled soils within microsites beneath native perennial bunchgrass and exotic annuals to characterize underlying soil microbial communities. High precipitation following seeding led to strong seedling establishment and we found few differences between seeding treatments established with either drill. All seeded treatments reduced exotic biomass by at least 90% relative to unseeded controls. Soil microbial communities (phospholipid fatty acid analysis), beneath B. tectorum, Poa secunda, and Pseudoroegneria spicata microsites differed little 3 years after fire. However, microbial abundance beneath P. spicata increased from June to July, suggesting that microbial communities beneath successful seedings can vary greatly within a single growing season.     

Microbial substrate preference and community dynamics during decomposition of Acer saccharum

The Guild Decomposition Model (GDM) hypothesized that temporal shifts in microbial “guilds,” each with distinct substrate preferences, drive decomposition dynamics and regulate soil carbon (C) losses and sequestration. To test this hypothesis, we established a laboratory incubation of Acer saccharum litter and monitored respiration, microbial biomass and enzyme activities, inorganic nutrients and shifts in functional groups of decomposers using phospholipid fatty acid (PLFA) analysis. Biomass and respiration peaked within the first 2 d of incubation, and the Gram negative PLFA biomarker 18:1ω7c predominated during the first 5 d. Hydrolytic enzyme activities and two fungal biomarkers (18:2ω6,9c and 18:3ω6c) increased by 25 d and lignolytic enzyme activity was detected at 68 d. Our results suggest that decomposers preferentially use labile substrates and that shifts in decomposer groups occur in response to changes in available substrates, which supports the GDM.