Characterization of Bacteria That Suppress Rhizoctonia Damping-Off in Bark Compost Media by Analysis of Fatty Acid Biomarkers

Depth-driven responses of microbial residual carbon to nitrogen addition approaches in a tropical forest: Canopy addition versus understory addition

Canopies play an important role in nitrogen (N) redistribution in forest ecosystems, and ignoring the canopy's role might bias estimates of the ecological consequences of anthropogenic atmospheric N deposition. We investigated the effects of the approach of N addition (Canopy addition vs. Understory addition) and level of N addition (25 kg N ha^-1yr^-1 vs. 50 kg N ha^-1yr^-1) on microbial residual carbon (MRC) accumulation in topsoil and subsoil. We found that the response of MRC to both approach and level of N addition varied greatly with soil depth in a tropical forest over eight years of continuous N addition. Specifically, N addition enhanced the accumulation of fungal and total MRC and their contribution to soil organic C (SOC) pools in the topsoil, whereas it decreased the contribution of fungal and total MRC to SOC in the subsoil. The contrasting effects of N addition on MRC contribution at varying soil depths were associated with the distinct response of microbial residues production. Understory N addition showed overall greater effects on MRC accumulation than canopy N addition did. Our results suggest that the canopy plays an important role in buffering the impacts of anthropogenic atmospheric N deposition on soil C cycling in tropical forests. The depth-dependent response of microbial residues to N addition also highlights the urgent need for further studies of different response mechanisms at different soil depths.

Assessment of CuO NPs on soil microbial community structure based on phospholipid fatty acid techniques and phytotoxicity of bok choy seedlings

In this study, a soil culture and a hydroponic experiment were conducted to assess the toxicology effects of copper oxide nanoparticles (CuO NPs) on soil microbial community structure and the growth of bok choy. Results showed CuO NPs had an inhibitory effect on soil microbial abundance, diversity, and activity, as well as the bok choy seedling growth, whereas CuO NPs at low concentrations did not significantly affect the soil microbial biomass or plant growth. In soil, CuO NPs at high dose (80 mg kg^-1) significantly reduced the indexes of Simpson diversity, Shannon-Wiener diversity and Pielou evenness by 3.7%, 4.9% and 4.5%, respectively. In addition, CuO NPs at 20 and 80 mg kg^-1 treatment significantly reduced soil enzymes (urease, alkaline phosphatase, dehydrogenase, and catalase) activities by 25.5%-58.9%. Further, CuO NPs at 20 mg L^-1 significantly inhibited the growth of plant root by 33.8%, and catalase (CAT) activity by 17.9% in bok choy seedlings. The present study can provide a basis for a comprehensive evaluation of the toxicity effect of CuO NPs on soil microorganisms and phytotoxicity to bok choy seedlings.

Nitrogen and phosphorus addition exerted different influences on litter and soil carbon release in a tropical forest

Terrestrial soils release large amount of carbon dioxide (CO₂) each year, which are mainly derived from litter and soil carbon (C) decomposition. Nutrient availability, especially nitrogen (N) and phosphorus (P), plays an important role in both litter and soil C decomposition. Therefore, understanding the underlying mechanism is crucial for mitigating CO₂ emission and climate changes. Here, we assessed patterns of litter and soil C decomposition after 11 yrs. in-situ N and P addition in a tropical forest where corn leaves or corn roots were added as litter C. The total CO₂ efflux was quantified and partitioned using ¹³C isotope signatures to determine the sources (litter or soil C) every three months. In addition, Changes in C-degrading enzyme activities: β-1,4-glucosidase (BG), phenol oxidase (PHO) and peroxidase (PER), and microbial biomarkers were assessed to interpret the underlying mechanism. Total C-release was enhanced up to17% by the long-term N addition but inhibited up to 15% by P addition. Precisely, N addition only accelerated the litter decomposition and increased about 42% and 6% of the litter C release at 0-5 cm and 5-10 cm soil depths, respectively; while P addition only impeded the soil C decomposition and decreased about 9% and 11% of the soil C release at 0-5 cm and 5-10 cm, respectively. The enhanced C release under N addition might be attributed to the enhanced microbial biomass, the ratio of fungi to bacteria and C-degrading enzyme activities. However, P addition resulted in the reverse result in microbial properties and C-degrading enzyme activities, associated with a decreased C release. Our study suggests that the long-term N and P addition selectively affected the litter and soil C decomposition because of their different physiochemical properties and this tendency might be more pronounced in tropical forests exposed to increasing atmospheric N deposition in the future. The study indicates that the different patterns of litter and soil C decomposition under climate change should be taken account in the future C management strategies.

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids

The distribution pattern of the microbial community in mountains is an important component of biodiversity research. Many environmental factors vary significantly with elevation on a relatively small scale in subalpine and alpine environments. These factors may markedly affect microbial community composition and function. In this study, we analyzed phospholipid fatty acid (PLFA) profiles and phosphorus (P) fractions in soils from 9 sites along an elevation gradient (3500–4100 m above sea level (a.s.l.)) of the Shergyla Mountain, Tibet in China. Many biomarker PLFAs indicated that there were biogeochemical trends of the microbial distribution patterns of some soil microorganisms, which were most often increasing, U-shaped and unimodal trends along the elevation gradient. A redundancy analysis (RDA) and correlations indicated that P factors (e.g., Resin-Pi, NaHCO₃-Pi and NaHCO₃-Po) were more important in controlling the microbial PLFA distribution pattern than other factors (e.g., MAT, MAP, pH, TOC, TN and soil moisture) in this study area. Microorganisms are strongly associated with P fractions. Our results suggested that microbial communities were subjected to P stresses and that the distribution patterns of microbial communities were shaped by bioavailable P along the elevation gradient. Our work also hints that P geochemical processes drive the microbial diversity of the Shergyla Mountains.

Long-term fertilization modifies the mineralization of soil organic matter in response to added substrate

The turnover of SOC in soils is strongly influenced by the availability of substrate and nutrients, especially nitrogen (N) and phosphorus (P). Here, we assessed how long-term fertilization modified SOM mineralization in response to added substrate in a tropical forest. We carried out a 90-day incubation study in which we added two structurally similar compounds which differed in microbial metabolic availability: corn cellulose or corn starch to soils collected from a long-term (11 years) factorial N and P fertilization experiment site in a tropical forest in south China. We measured total soil mineralization rate (CO₂ efflux) to characterize SOM mineralization and using ¹³C isotope signatures to determine the source of the CO₂ (original soil C or added substrate) and assessed changes in extracellular enzyme activities: acid phosphomonoesterase (AP), β-1,4-glucosidase (BG), β-1,4- N-acetaminophen glucosidase (NAG), phenol oxidase (PHO) and peroxidase (PER), and microbial biomarkers to determine whether nutrient stoichiometry and decomposer communities explain differences in SOM mineralization rates. Total C mineralization increased substantially with substrate addition, particularly cellulose (5.38, 7.13, 5.58 and 5.37 times for N, P, NP fertilization and CK, respectively) compared to no substrate addition, and original soil C mineralization was further enhanced in long-term N (3.40% and 5.18% for cellulose and starch addition, respectively) or NP (35.11% for cellulose addition) fertilized soils compared to control treatment. Enzyme activities were stimulated by the addition of both substrates but suppressed by P-fertilization. Addition of both substrates increased microbial investment in P-acquisition, but only starch addition promoted C investment in N-acquisition. Finally, fungal abundance increased with substrate addition to a greater extent than bacterial abundance, particularly in cellulose-amended soils, and the effect was amplified by long-term fertilization. Our findings indicate that SOM mineralization might be enhanced in N and P enrichment ecosystems, since the litter input can liberate microbes from C limitation and stimulate SOM mineralization if N and P are sufficient. Our study further demonstrates that structurally similar substrates can have distinct effects on SOM mineralization and the extent of SOM mineralization is strongly dependent on elemental stoichiometry, as well as the resource requirements of microbial decomposers.

Plant and microbial regulations of soil carbon dynamics under warming in two alpine swamp meadow ecosystems on the Tibetan Plateau

Increasing temperature plays important roles in affecting plant and soil microbial communities as well as ecological processes and functions in terrestrial ecosystems. However, mechanisms of warming influencing soil carbon dynamics associated with plant-microbe interactions remain unclear. In this study, open-top chambers (OTCs) experiments were carried out to detect the responses of plants, soil microbes, and SOC contents, physical fractions (by particle-size fractionation) and chemical composition (by solid-state ¹³C NMR spectroscopy) to warming in two alpine swamp meadows (Kobresia humilis vs K. tibetica) on the Tibetan Plateau. Our results showed that four years of warming had significant influences on plant belowground biomass, microbial community and SOC contents in the K. humilis swamp meadow, but had much weaker or minor effects in the K. tibetica swamp meadow with water-logged status and lower level of warming. In the K. humilis swamp meadow, warming increased microbial biomass, C-hydrolysis gene abundance and N-acetylglucosaminidase enzyme activity. These positive effects of warming on microbial biomass and functions further increased soil dissolved inorganic nitrogen and alleviated the nitrogen limitation for plant growth, potentially leading to higher plant biomass. Therefore, increases in SOC and particulate organic carbon (POC) under warming were likely attributed to the higher C input with promoted plant biomass overweighting the simultaneous higher C degradation and release in the K. humilis swamp meadow. Conversely, warming marginally reduced soil alkyl C, which was likely associated with enhanced decomposition by fungi and gram-positive bacteria. Overall, the increases in unprotected POC and decreases in recalcitrant alkyl C demonstrate the sensitivity of SOC physical fractions as well as chemical composition to climate warming in the K. humilis alpine swamp meadow, and suggest that the overall stability of SOC might be lower despite the gain in the content of SOC after climate warming in this alpine swamp meadow.

Soil Microbial Community Based on PLFA Profiles in an Age Sequence of Pomegranate Plantation in the Middle Yellow River Floodplain

Pomegranate (Punica granatum L.) is one of the most important fruit trees in semi-arid land. Previous studies were primarily focused on soil microbial community composition under different pomegranate plantation managements. However, soil microbial community composition under long-term pomegranate plantation has rarely been studied. We investigated pomegranate plantation along with an age sequence (i.e., 1, 3, 5, and 10 years after pomegranate plantation; abbreviated by P1, P3, P5, P10, respectively) in the Middle Yellow River floodplain. Our objectives were to address (1) variations of soil physicochemical properties and (2) changes in soil microbial community composition and the influential factors. The results demonstrated that the soil water content of pomegranate plantation decreased with the increase of pomegranate plantation stand age. Specifically, dissolved organic carbon, ammonium, and available phosphorus increased significantly with stand age both at 0–10- and 10–20-cm soil depths. The P10 had the highest microbial phospholipid fatty acid (PLFA) profiles, including fungi, bacteria, Gram-positive bacteria, Gram-negative bacteria, and arbuscular mycorrhizal fungi. The ratio of fungal PLFAs to bacterial PLFAs increased and the ratio of Gram-positive to Gram-negative bacterial PLFAs decreased along the pomegranate plantation stand age. Dissolved organic carbon was the most important influential factor among the studied variables, which explained 42.2% variation of soil microbial community. In summary, the long-term plantation of pomegranate elevated soil microbial biomass and altered microbial community composition.

Excessive nitrogen addition accelerates N assimilation and P utilization by enhancing organic carbon decomposition in a Tibetan alpine steppe

High amounts of deposited nitrogen (N) dramatically influence the stability and functions of alpine ecosystems by changing soil microbial community functions, but the mechanism is still unclear. To investigate the impacts of increased N deposition on microbial community functions, a 2-year multilevel N addition (0, 10, 20, 40, 80 and 160 kg N ha^-1 year^-1) field experiment was set up in an alpine steppe on the Tibetan Plateau. Soil microbial functional genes (GeoChip 4.6), together with soil enzyme activity, soil organic compounds and environmental variables, were used to explore the response of microbial community functions to N additions. The results showed that the N addition rate of 40 kg N ha^-1 year^-1 was the critical value for soil microbial functional genes in this alpine steppe. A small amount of added N (≤40 kg N ha^-1 year^-1) had no significant effects on the abundance of microbial functional genes, while high amounts of added N (>40 kg N ha^-1 year^-1) significantly increased the abundance of soil organic carbon degradation genes. Additionally, the abundance of microbial functional genes associated with NH₄⁺, including ammonification, N fixation and assimilatory nitrate reduction pathways, was significantly increased under high N additions. Further, high N additions also increased soil organic phosphorus utilization, which was indicated by the increase in the abundance of phytase genes and alkaline phosphatase activity. Plant richness, soil NO₂^-/NH₄⁺ and WSOC/WSON were significantly correlated with the abundance of microbial functional genes, which drove the changes in microbial community functions under N additions. These findings help us to predict that increased N deposition in the future may alter soil microbial functional structure, which will lead to changes in microbially-mediated biogeochemical dynamics in alpine steppes on the Tibetan Plateau and will have extraordinary impacts on microbial C, N and P cycles.

Epiphytic Microbial Diversity of Vitis vinifera Fructosphere: Present Status and Potential Applications

Vineyard provides an apt environment for growth of different types of microorganisms. The microbial domain is greatly affected by changing climatic conditions, geographical region, water activity, agricultural practices, presence of different pathogens and various pests. Grapevine microbial diversity is also affected by different stages of plant growth. Epiphytic berry microflora is specifically influenced by developmental phases and plays an important role in winemaking which is studied extensively. However, very little information is available about microbial community associated with table grape berries, which are consumed as fresh fruits. Moreover, our knowledge about the important role played by these microbes is precise and their scope might be larger than what is existing in the public domain. A systematic study on effect of developmental stages of table grape berries on microbial diversity would provide new insights for exploring the applicability of these microbes in plant growth, crop protection and bioremediation. In this review, we propose an effort to relate the developmental stages of grape berry with microbial consortium present and at the same time discuss the possible applications of these microbes in plant protection and biodegradation.

Responses of litter, organic and mineral soil enzyme kinetics to 6 years of canopy and understory nitrogen additions in a temperate forest

Increasing atmospheric nitrogen (N) deposition could profoundly impact soil carbon, N and phosphorus cycling that are often regulated by extracellular enzymes. The potential activities of enzymes in response to N deposition have been studied extensively, but the kinetic mechanisms in response to canopy and understory N additions in different soil layers are poorly understood. Here, we conducted a six-year-long field manipulation experiment in a temperate deciduous forest to reveal the kinetic characteristics of seven extracellular hydrolytic enzymes in the litter, organic and mineral soil layers in response to canopy and understory N additions. Canopy N addition and understory N addition exerted similar effects on the kinetics parameters (V_max and K_m) of most enzymes under study. The kinetics parameters of most enzymes generally increased in the litter layer but decreased in the organic layer and had little change in the mineral soil layer in response to N addition. In addition, the changed kinetic parameters were mainly correlated with moisture in the litter layer, with pH, substrate properties (TC, TN, DOC and DON) and microbial communities (G⁺, G^-, total bacterial and fungal biomass) in the organic and mineral soil layers. These findings indicate that enzyme kinetics responses to N deposition differ in soil layers with varying determinant factors, and therefore are driven by various physical, chemical and microbial mechanisms.

Effects of seasonal precipitation change on soil respiration processes in a seasonally dry tropical forest

Precipitation is projected to change intensity and seasonal regime under current global projections. However, little is known about how seasonal precipitation changes will affect soil respiration, especially in seasonally dry tropical forests. In a seasonally dry tropical forest in South China, we conducted a precipitation manipulation experiment to simulate a delayed wet season (DW) and a wetter wet season (WW) over a three-year period. In DW, we reduced 60% throughfall in April and May to delay the onset of the wet season and irrigated the same amount water into the plots in October and November to extend the end of the wet season. In WW, we irrigated 25% annual precipitation into plots in July and August. A control treatment (CT) receiving ambient precipitation was also established. Compared with CT, DW significantly increased soil moisture by 54% during October to November, and by 30% during December to April. The treatment of WW did not significantly affect monthly measured soil moisture. In 2015, DW significantly increased leaf area index and soil microbial biomass but decreased fine root biomass. In contrast, WW significantly decreased fine root biomass and forest floor litter stocks. Soil respiration was not affected by DW, which could be attributed to the increased microbial biomass offsetting the decrease in fine root biomass. In contrast, WW significantly increased soil respiration from 3.40 to 3.90 μmol m-2 s-1 in the third year, mainly due to the increased litter decomposition and soil pH (from 4.48 to 4.68). The present study suggests that both a delayed wet season and a wetter wet season will have significant impacts on soil respiration-associated ecosystem components. However, the ecosystem components can respond in different directions to the same change in precipitation, which ultimately affected soil respiration.

Effects of urbanization on plant phosphorus availability in broadleaf and needleleaf subtropical forests

Urbanization, the migration of populations from rural to urban areas, has been causing great stress on natural environments, leading to air pollution and nitrogen (N) deposition, negatively affecting forest health. Although there is evidence that urbanization has changed forest N cycling, little is known about whether urbanization also changes the availability of phosphorus (P), which is important for plant growth and forest productivity. To address this question, we carried out a survey in the Pearl River Delta region, the world's largest urban area in southern China, using two types of representative forests, the evergreen broadleaf forests (BFs) and pine plantations (PPs). The leaf N:P ratios in the two forest types were high (20-50) with a significant increasing pattern along the rural-to-urban gradient. The ratios of leaf P:K and P:Na declined along the rural-to-urban gradient, whereas leaf P content did not change in BF but decreased in PP along the rural-to-urban gradient, suggesting that leaf P became limiting along urbanization. The abundance of actinomycetes and gram-negative bacteria decreased along the rural-to-urban gradient, indicating the negative effects of urbanization on soil microorganisms. Principal component analysis indicated that divergent key factors respond to the urbanization and affect plant P limitation in the two forest types. In BF, broadleaf trees showed a greater response to N deposition from urbanization indicating direct leaf N uptake from N deposition is a key factor for plant P limitation. Alternatively, in PP, our findings suggest soil acidification is an important factor accelerating plant P limitation. Our study revealed that urbanization intensifies plant P limitation in subtropical forests, and the effects vary depending on forest types. Our findings provide empirical information to support the management of forest ecosystems and evaluation of urbanization effects on forest health.

The influence of chlorination timing and concentration on microbial communities in labyrinth channels: implications for biofilm removal

Chlorination is an effective method to control biofilm formation in enclosed pipelines. To date, very little is known about how to control biofilms at the mesoscale in complex pipelines through chlorination. In this study, the dynamic of microbial communities was examined under different residual chlorine concentrations on the biofilms attached to labyrinth channels for drip irrigation using reclaimed water. The results indicated that the microbial phospholipid fatty acids, extracellular polymeric substances, microbial dynamics, and the ace and Shannon microbial diversity indices showed a gradual decrease after chlorination. However, chlorination increased microbial activity by 0.5-19.2%. The increase in the relative abundances of chloride-resistant bacteria (Acinetobacter and Thermomonas) could lead to a potential risk of chlorine resistance. Thus, keeping a low chlorine concentration (0.83 mg l^-1 for 3 h) is effective for controlling biofilm formation in the labyrinth channels.

Towards frailty biomarkers: Candidates from genes and pathways regulated in aging and age-related diseases

OBJECTIVE

Use of the frailty index to measure an accumulation of deficits has been proven a valuable method for identifying elderly people at risk for increased vulnerability, disease, injury, and mortality. However, complementary molecular frailty biomarkers or ideally biomarker panels have not yet been identified. We conducted a systematic search to identify biomarker candidates for a frailty biomarker panel.

METHODS

Gene expression databases were searched (http://genomics.senescence.info/genes including GenAge, AnAge, LongevityMap, CellAge, DrugAge, Digital Aging Atlas) to identify genes regulated in aging, longevity, and age-related diseases with a focus on secreted factors or molecules detectable in body fluids as potential frailty biomarkers. Factors broadly expressed, related to several "hallmark of aging" pathways as well as used or predicted as biomarkers in other disease settings, particularly age-related pathologies, were identified. This set of biomarkers was further expanded according to the expertise and experience of the authors. In the next step, biomarkers were assigned to six "hallmark of aging" pathways, namely (1) inflammation, (2) mitochondria and apoptosis, (3) calcium homeostasis, (4) fibrosis, (5) NMJ (neuromuscular junction) and neurons, (6) cytoskeleton and hormones, or (7) other principles and an extensive literature search was performed for each candidate to explore their potential and priority as frailty biomarkers.

RESULTS

A total of 44 markers were evaluated in the seven categories listed above, and 19 were awarded a high priority score, 22 identified as medium priority and three were low priority. In each category high and medium priority markers were identified.

CONCLUSION

Biomarker panels for frailty would be of high value and better than single markers. Based on our search we would propose a core panel of frailty biomarkers consisting of (1) CXCL10 (C-X-C motif chemokine ligand 10), IL-6 (interleukin 6), CX3CL1 (C-X3-C motif chemokine ligand 1), (2) GDF15 (growth differentiation factor 15), FNDC5 (fibronectin type III domain containing 5), vimentin (VIM), (3) regucalcin (RGN/SMP30), calreticulin, (4) PLAU (plasminogen activator, urokinase), AGT (angiotensinogen), (5) BDNF (brain derived neurotrophic factor), progranulin (PGRN), (6) α-klotho (KL), FGF23 (fibroblast growth factor 23), FGF21, leptin (LEP), (7) miRNA (micro Ribonucleic acid) panel (to be further defined), AHCY (adenosylhomocysteinase) and KRT18 (keratin 18). An expanded panel would also include (1) pentraxin (PTX3), sVCAM/ICAM (soluble vascular cell adhesion molecule 1/Intercellular adhesion molecule 1), defensin α, (2) APP (amyloid beta precursor protein), LDH (lactate dehydrogenase), (3) S100B (S100 calcium binding protein B), (4) TGFβ (transforming growth factor beta), PAI-1 (plasminogen activator inhibitor 1), TGM2 (transglutaminase 2), (5) sRAGE (soluble receptor for advanced glycosylation end products), HMGB1 (high mobility group box 1), C3/C1Q (complement factor 3/1Q), ST2 (Interleukin 1 receptor like 1), agrin (AGRN), (6) IGF-1 (insulin-like growth factor 1), resistin (RETN), adiponectin (ADIPOQ), ghrelin (GHRL), growth hormone (GH), (7) microparticle panel (to be further defined), GpnmB (glycoprotein nonmetastatic melanoma protein B) and lactoferrin (LTF). We believe that these predicted panels need to be experimentally explored in animal models and frail cohorts in order to ascertain their diagnostic, prognostic and therapeutic potential.

Plant-facilitated effects of exotic earthworm Pontoscolex corethrurus on the soil carbon and nitrogen dynamics and soil microbial community in a subtropical field ecosystem

Earthworms and plants greatly affect belowground properties; however, their combined effects are more attractive based on the ecosystem scale in the field condition. To address this point, we manipulated earthworms (exotic endogeic species Pontoscolex corethrurus) and plants (living plants [native tree species Evodia lepta] and artificial plants) to investigate their combined effects on soil microorganisms, soil nutrients, and soil respiration in a subtropical forest. The manipulation of artificial plants aimed to simulate the physical effects of plants (e.g., shading and interception of water) such that the biological effects of plants could be evaluated separately. We found that relative to the controls, living plants but not artificial plants significantly increased the ratio of fungal to bacterial phospholipid fatty acids (PLFAs) and fungal PLFAs. Furthermore, earthworms plus living plants significantly increased the soil respiration and decreased the soil NH₄⁺‐N, which indicates that the earthworm effects on the associated carbon, and nitrogen processes were greatly affected by living plants. The permutational multivariate analysis of variance results also indicated that living plants but not earthworms or artificial plants significantly changed the soil microbial community. Our results suggest that the effects of plants on soil microbes and associated soil properties in this study were largely explained by their biological rather than their physical effects.

Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa

Understanding the abundance change of certain bacterial taxa is quite important for the study of soil microbiology. However, the observed differences of relative abundances by high-throughput techniques may not accurately reflect those of the actual taxon abundances. This study investigated whether soil microbial abundances coupling with microbial quantities can be more informative in describing the microbial population distribution under different locations. We analyzed relative abundances of the major species in soil microbial communities from Beijing and Tibet grasslands by using 16 S rRNA high-throughput sequencing technique, and quantified the absolute bacterial cell numbers directly or indirectly by multiple culture-independent measurements, including adenosine tri-phosphate (ATP), flow cytometry (FCM), quantitative real-time PCR (qPCR), phospholipid fatty acids (PLFA) and microbial biomass Carbon (MBC). By comparison of the relative abundance and the estimated absolute abundances (EAA) of the major components in soil microbial communities, several dominant phyla, including Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonates and Planctomycetes, showed significantly different trends. These results indicated that the change in EAA might be more informative in describing the dynamics of a population in a community. Further studies of soil microbes should combine the quantification and relative abundances of the microbial communities for the comparisons among various locations.

Sampling Terrestrial Environments for Bacterial Polyketides

Bacterial polyketides are highly biologically active molecules that are frequently used as drugs, particularly as antibiotics and anticancer agents, thus the discovery of new polyketides is of major interest. Since the 1980s discovery of polyketides has slowed dramatically due in large part to the repeated rediscovery of known compounds. While recent scientific and technical advances have improved our ability to discover new polyketides, one key area has been under addressed, namely the distribution of polyketide-producing bacteria in the environment. Identifying environments where producing bacteria are abundant and diverse should improve our ability to discover (bioprospect) new polyketides. This review summarizes for the bioprospector the state-of-the-field in terrestrial microbial ecology. It provides insight into the scientific and technical challenges limiting the application of microbial ecology discoveries for bioprospecting and summarizes key developments in the field that will enable more effective bioprospecting. The major recent efforts by researchers to sample new environments for polyketide discovery is also reviewed and key emerging environments such as insect associated bacteria, desert soils, disease suppressive soils, and caves are highlighted. Finally strategies for taking and characterizing terrestrial samples to help maximize discovery efforts are proposed and the inclusion of non-actinomycetal bacteria in any terrestrial discovery strategy is recommended.

Atrazine contamination in agricultural soils from the Yangtze River Delta of China and associated health risks

Atrazine is one of the most widely applied and persistent herbicides in the world. In view of limited information on the regional contamination of atrazine in soils in China, this study investigated the spatial distribution and environmental impacts of atrazine in agricultural soils collected from the Yangtze River Delta (YRD) as an illustrative analysis of rapidly developing regions in the country. The results showed that the concentrations of atrazine in the YRD agricultural soils ranged from <1.0 to 113 ng/g dry weight, with a mean of 5.7 ng/g, and a detection rate of 57.7 % in soils. Pesticide factory might be a major source for the elevated levels of atrazine in Zhejiang Province. The contamination of atrazine was closely associated with land use types. The concentrations and detection rates of atrazine were higher in corn fields and mulberry fields than in rice paddy fields. There was no significant difference in compositions of soil microbial phospholipids fatty acids among the areas with different atrazine levels. Positive relationship (R = 0.417, p < 0.05, n = 30) was observed between atrazine and total microbial biomass. However, other factors, such as soil type and land management practice, might have stronger influences on soil microbial communities. Human health risks via exposure to atrazine in soils were estimated according to the methods recommended by the US EPA. Atrazine by itself in all the soil samples imposed very low carcinogenic risks (<10^-6) and minimal non-cancer risks (hazard index <1) to adults and children.

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

Phospholipid fatty acids (PLFAs) are key components of microbial cell membranes. The analysis of PLFAs extracted from soils can provide information about the overall structure of terrestrial microbial communities. PLFA profiling has been extensively used in a range of ecosystems as a biological index of overall soil quality, and as a quantitative indicator of soil response to land management and other environmental stressors.

The standard method presented here outlines four key steps: 1. lipid extraction from soil samples with a single-phase chloroform mixture, 2. fractionation using solid phase extraction columns to isolate phospholipids from other extracted lipids, 3. methanolysis of phospholipids to produce fatty acid methyl esters (FAMEs), and 4. FAME analysis by capillary gas chromatography using a flame ionization detector (GC-FID). Two standards are used, including 1,2-dinonadecanoyl-sn-glycero-3-phosphocholine (PC(19:0/19:0)) to assess the overall recovery of the extraction method, and methyl decanoate (MeC10:0) as an internal standard (ISTD) for the GC analysis.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Different soil respiration responses to litter manipulation in three subtropical successional forests

Aboveground litter inputs have been greatly altered by human disturbances and climate change, which have important effects on soil respiration. However, the knowledge of how soil respiration responds to altered litter inputs is limited in tropical and subtropical forests. We conducted an aboveground litterfall manipulation experiment in three successional forests in the subtropics to examine the soil respiration responses to different litter inputs from January 2010 to July 2012. The soil respiration decreased by 35% in the litter exclusion treatments and increased by 77% in the doubled litter additions across all three forests. The reduction in soil respiration induced by the litter exclusion was greatest in the early successional forest, which may be related to a decrease in the soil moisture and shifts in the microbial community. The increase in soil respiration produced by the doubled litter addition was largest in the mature forest, which was most probably due to its relatively high quantity and quality of litterfall. Our results suggest that the effect of reduced litter inputs on the soil respiration lessened with forest succession but that the doubled litter inputs resulted in a stronger priming effect in the mature forest than in the other two forests.

Effects of nitrogen and phosphorus additions on soil microbial biomass and community structure in two reforested tropical forests

Elevated nitrogen (N) deposition may aggravate phosphorus (P) deficiency in forests in the warm humid regions of China. To our knowledge, the interactive effects of long-term N deposition and P availability on soil microorganisms in tropical replanted forests remain unclear. We conducted an N and P manipulation experiment with four treatments: control, N addition (15 g N m⁻²·yr⁻¹), P addition (15 g P m⁻²·yr⁻¹), and N and P addition (15 + 15 g N and P m⁻²·yr⁻¹, respectively) in disturbed (planted pine forest with recent harvests of understory vegetation and litter) and rehabilitated (planted with pine, but mixed with broadleaf returning by natural succession) forests in southern China. Nitrogen addition did not significantly affect soil microbial biomass, but significantly decreased the abundance of gram-negative bacteria PLFAs in both forest types. Microbial biomass increased significantly after P addition in the disturbed forest but not in the rehabilitated forest. No interactions between N and P additions on soil microorganisms were observed in either forest type. Our results suggest that microbial growth in replanted forests of southern China may be limited by P rather than by N, and this P limitation may be greater in disturbed forests.

Anthropogenic nitrogen deposition enhances carbon sequestration in boreal soils

It is proposed that carbon (C) sequestration in response to reactive nitrogen (Nr ) deposition in boreal forests accounts for a large portion of the terrestrial sink for anthropogenic CO2 emissions. While studies have helped clarify the magnitude by which Nr deposition enhances C sequestration by forest vegetation, there remains a paucity of long-term experimental studies evaluating how soil C pools respond. We conducted a long-term experiment, maintained since 1996, consisting of three N addition levels (0, 12.5, and 50 kg N ha(-1) yr(-1) ) in the boreal zone of northern Sweden to understand how atmospheric Nr deposition affects soil C accumulation, soil microbial communities, and soil respiration. We hypothesized that soil C sequestration will increase, and soil microbial biomass and soil respiration will decrease, with disproportionately large changes expected compared to low levels of N addition. Our data showed that the low N addition treatment caused a non-significant increase in the organic horizon C pool of ~15% and a significant increase of ~30% in response to the high N treatment relative to the control. The relationship between C sequestration and N addition in the organic horizon was linear, with a slope of 10 kg C kg(-1) N. We also found a concomitant decrease in total microbial and fungal biomasses and a ~11% reduction in soil respiration in response to the high N treatment. Our data complement previous data from the same study system describing aboveground C sequestration, indicating a total ecosystem sequestration rate of 26 kg C kg(-1) N. These estimates are far lower than suggested by some previous modeling studies, and thus will help improve and validate current modeling efforts aimed at separating the effect of multiple global change factors on the C balance of the boreal region.

Comparative study of microbial community structure in integrated vertical-flow constructed wetlands for treatment of domestic and nitrified wastewaters

Microbial processes play a vital important role in the removal of contaminants in constructed wetland (CW). However, the microbial physiology and community structure can be influenced by environmental conditions. In this study, four pilot-scale integrated vertical-flow constructed wetlands (IVCWs) were employed to treat domestic and nitrified wastewaters. The microbial properties, along with their response to wastewater quality characteristics and seasonal variation, were determined. The results showed higher Shannon-Weiner diversity (H) and evenness (E) index of fatty acids (FAs), and relative abundances of signature FAs in down-flow cells and in the systems fed with domestic wastewater (DW). The relative abundances of fungi and gram-negative and aerobic bacteria were greater in up-flow cells. The dominant anaerobic bacteria found in most cells might be accounted for the prevailing anaerobic environment within the wetland beds, which could mean that the system fed with nitrified wastewater (NW) should perform better in nitrogen removal. The redundancy analysis (RDA) showed that pollutant concentrations, especially organic matter, influence the FA compositions greatly, and the most significant difference of microbial community structures was detected in down-flow cells fed with DW and up-flow ones with NW. The branched FAs, which could be used to represent anaerobic bacteria, were observed in down-flow cells treating DW and had a significant positive correlation with chemical oxygen demand (COD) concentration, probably suggesting the important role of anaerobic bacteria in organic matter degradation in the IVCWs. Seasonal variation, however, did not greatly influence the microbial community structure in the IVCWs.

Impact of plant species evenness, dominant species identity and spatial arrangement on the structure and functioning of soil microbial communities in a model grassland

Plant communities, through species richness and composition, strongly influence soil microorganisms and the ecosystem processes they drive. To test the effects of other plant community attributes, such as the identity of dominant plant species, evenness, and spatial arrangement, we set up a model mesocosm experiment that manipulated these three attributes in a full factorial design, using three grassland plant species (Anthoxanthum odoratum, Plantago lanceolata, and Lotus corniculatus). The impact of the three community attributes on the soil microbial community structure and functioning was evaluated after two growing seasons by ester-linked phospholipid fatty-acids analysis, substrate-induced respiration, basal respiration, and nitrogen mineralization and nitrification rates. Our results suggested that the dominant species identity had the most prevalent influence of the three community attributes, with significant effects on most of the measured aspects of microbial biomass, composition and functioning. Evenness had no effects on microbial community structure, but independently influenced basal respiration. Its effects on nitrogen cycling depended on the identity of the dominant plant species, indicating that interactions among species and their effects on functioning can vary with their relative abundance. Systems with an aggregated spatial arrangement had a different microbial community composition and a higher microbial biomass compared to those with a random spatial arrangement, but rarely differed in their functioning. Overall, it appears that dominant species identity was the main driver of soil microorganisms and functioning in these model grassland communities, but that other plant community attributes such as evenness and spatial arrangement can also be important.

Aboveground and belowground legacies of native Sami land use on boreal forest in northern Sweden 100 years after abandonment

Human activities that involve land-use change often cause major transformations to community and ecosystem properties both aboveground and belowground, and when land use is abandoned, these modifications can persist for extended periods. However, the mechanisms responsible for rapid recovery vs. long-term maintenance of ecosystem changes following abandonment remain poorly understood. Here, we examined the long-term ecological effects of two remote former settlements, regularly visited for -300 years by reindeer-herding Sami and abandoned -100 years ago, within an old-growth boreal forest that is considered one of the most pristine regions in northern Scandinavia. These human legacies were assessed through measurements of abiotic and biotic soil properties and vegetation characteristics at the settlement sites and at varying distances from them. Low-intensity land use by Sami is characterized by the transfer of organic matter towards the settlements by humans and reindeer herds, compaction of soil through trampling, disappearance of understory vegetation, and selective cutting of pine trees for fuel and construction. As a consequence, we found a shift towards early successional plant species and a threefold increase in soil microbial activity and nutrient availability close to the settlements relative to away from them. These changes in soil fertility and vegetation contributed to 83% greater total vegetation productivity, 35% greater plant biomass, and 23% and 16% greater concentrations of foliar N and P nearer the settlements, leading to a greater quantity and quality of litter inputs. Because decomposer activity was also 40% greater towards the settlements, soil organic matter cycling and nutrient availability were further increased, leading to likely positive feedbacks between the aboveground and belowground components resulting from historic land use. Although not all of the activities typical of Sami have left visible residual traces on the ecosystem after 100 years, their low-intensity but long-term land use at settlement sites has triggered a rejuvenation of the ecosystem that is still present. Our data demonstrates that aboveground-belowground interactions strongly control ecosystem responses to historical human land use and that medium- to long-term consequences of even low-intensity human activities must be better accounted for if we are to predict and manage ecosystems succession following land-use abandonment.

Effects of experimental nitrogen and phosphorus addition on litter decomposition in an old-growth tropical forest

The responses of litter decomposition to nitrogen (N) and phosphorus (P) additions were examined in an old-growth tropical forest in southern China to test the following hypotheses: (1) N addition would decrease litter decomposition; (2) P addition would increase litter decomposition, and (3) P addition would mitigate the inhibitive effect of N addition. Two kinds of leaf litter, Schima superba Chardn. & Champ. (S.S.) and Castanopsis chinensis Hance (C.C.), were studied using the litterbag technique. Four treatments were conducted at the following levels: control, N-addition (150 kg N ha⁻¹ yr⁻¹), P-addition (150 kg P ha⁻¹ yr⁻¹) and NP-addition (150 kg N ha⁻¹ yr⁻¹ plus 150 kg P ha⁻¹ yr⁻¹). While N addition significantly decreased the decomposition of both litters, P addition significantly inhibited decomposition of C.C., but did not affect the decomposition of S.S. The negative effect of N addition on litter decomposition might be related to the high N-saturation in this old-growth tropical forest; however, the negative effect of P addition might be due to the suppression of “microbial P mining”. Significant interaction between N and P addition was found on litter decomposition, which was reflected by the less negative effect in NP-addition plots than those in N-addition plots. Our results suggest that P addition may also have negative effect on litter decomposition and that P addition would mitigate the negative effect of N deposition on litter decomposition in tropical forests.

Interactive effects of nitrogen and phosphorus on soil microbial communities in a tropical forest

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of the microbial community, (3) the addition of N and P will have interactive effects on soil microbes and (4) addition-mediated changes in microbial communities would feed back on soil C pools. Phospholipid fatty acid (PLFA) analysis was used to quantify the soil microbial community following four treatments: Control, N addition (15 g N m(-2) yr(-1)), P addition (15 g P m(-2) yr(-1)), and N&P addition (15 g N m(-2) yr(-1) plus 15 g P m(-2) yr(-1)). These were applied from 2007 to 2011. Whereas additions of P increased soil microbial biomass, additions of N reduced soil microbial biomass. These effects, however, were transient, disappearing over longer periods. Moreover, N additions significantly increased relative abundance of fungal PLFAs and P additions significantly increased relative abundance of arbuscular mycorrhizal (AM) fungi PLFAs. Nitrogen addition had a negative effect on light fraction C, but no effect on heavy fraction C and total soil C. In contrast, P addition significantly decreased both light fraction C and total soil C. However, there were no interactions between N addition and P addition on soil microbes. Our results suggest that these nutrients are not co-limiting, and that P rather than N is limiting in this tropical forest.

Drivers of inter-year variability of plant production and decomposers across contrasting island ecosystems

Despite the likely importance of inter-year dynamics of plant production and consumer biota for driving community- and ecosystem-level processes, very few studies have explored how and why these dynamics vary across contrasting ecosystems. We utilized a well-characterized system of 30 lake islands in the boreal forest zone of northern Sweden across which soil fertility and productivity vary considerably, with larger islands being more fertile and productive than smaller ones. In this system we assessed the inter-year dynamics of several measures of plant production and the soil microbial community (primary consumers in the decomposer food web) for each of nine years, and soil microfaunal groups (secondary and tertiary consumers) for each of six of those years. We found that, for measures of plant production and each of the three consumer trophic levels, inter-year dynamics were strongly affected by island size. Further, many variables were strongly affected by island size (and thus bottom-up regulation by soil fertility and resources) in some years, but not in other years, most likely due to inter-year variation in climatic conditions. For each of the plant and microbial variables for which we had nine years of data, we also determined the inter-year coefficient of variation (CV), an inverse measure of stability. We found that CVs of some measures of plant productivity were greater on large islands, whereas those of other measures were greater on smaller islands; CVs of microbial variables were unresponsive to island size. We also found that the effects of island size on the temporal dynamics of some variables were related to inter-year variability of macroclimatic variables. As such, our results show that the inter-year dynamics of both plant productivity and decomposer biota across each of three trophic levels, as well as the inter-year stability of plant productivity, differ greatly across contrasting ecosystems, with potentially important but largely overlooked implications for community and ecosystem processes.

Structure and composition of biological slimes on paper and board machines

Biological slimes (biofilms) collected from the wet end of paper and board machines were examined by electron microscopy and analyzed for fatty acid composition, neutral sugar composition, and ATP. Electron microscopy revealed minuscule prokaryotic organisms (diameter, 0.2 to 0.4 mum). Larger cells morphologically resembling Sphaerotilus and Leptothrix spp. were found in slimes from machines using recycled fiber or unbleached pulp. The bacteria were embedded in a slimy matrix and often contained reserve materials microscopically resembling poly-beta-hydroxybutyrate and glycogen. Fatty acid analysis of the slimes revealed bacterial signature fatty acids in concentrations equivalent to the presence of 2 x 10 to 2.6 x 10 (average, 7 x 10) bacterial cells (live and dead) per g (dry weight) of slime. The slimes contained several known components of bacterial polysaccharides in addition to glucose, indicating that the slime body consisted of bacterial polysaccharides. The slimes contained uronic acids equivalent to a binding capacity of 12.5 to 50 mumol of divalent cations per g (dry weight) of slime. The uronic acid-containing polysaccharides may be responsible for the accumulation of heavy metals in the slime. Calculation of the ATP contents of the slimes resulted in an estimate of 5 x 10 cells per g (dry weight) of slime when calibrated with pure bacterial cultures isolated from the slimes. From electron micrographs, an estimate ranging from 1 x 10 to 1.5 x 10 (average, 4 x 10) cells per g (dry weight) of slime was obtained.

Soil Bacterial Biomass, Activity, Phospholipid Fatty Acid Pattern, and pH Tolerance in an Area Polluted with Alkaline Dust Deposition

Soil bacterial biomass, phospholipid fatty acid pattern, pH tolerance, and growth rate were studied in a forest area in Finland that is polluted with alkaline dust from an iron and steel works. The pollution raised the pH of the humus layer from 4.1 to 6.6. Total bacterial numbers and the total amounts of bacterial phospholipid fatty acids in the humus layer did not differ between the unpolluted control sites and the polluted ones. The number of CFU increased by a factor of 6.4 in the polluted sites compared with the controls, while the bacterial growth rate, measured by the thymidine incorporation technique, increased about 1.8-fold in the polluted sites. A shift in the pattern of phospholipid fatty acids indicated a shift in the bacterial species composition. The largest proportional increase was found for the fatty acid 10Me18:0, which indicated an increase in the number of actinomycetes in the polluted sites. The levels of the fatty acids i14:0, 16:1omega5, cy17:0, 18:1omega7, and 19:1 also increased in the polluted sites while those of fatty acids 15:0, i15:0, 10Me16:0, 16:1omega7t, 18:1omega9, and cy19:0 decreased compared with the unpolluted sites. An altered pH tolerance of the bacterial assemblage was detected either as a decrease in acid-tolerant CFU in the polluted sites or as altered bacterial growth rates at different pHs. The latter was estimated by measuring the thymidine incorporation rate of bacteria extracted from soil by homogenization-centrifugation at different pHs.

The impact of grassland management regime on the community structure of selected bacterial groups in soils

The impact of long-term grassland management regimes on microbial community structure in soils was assessed using multivariate analysis of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) banding patterns of selected bacterial groups and PLFA (phospholipid fatty acid) profiling. The management regimes assessed were inorganic nitrogen (N) fertiliser application and soil drainage. PCR-DGGE profiles of the eubacteria, actinomycetes, ammonia oxidisers and pseudomonads were assessed by principal co-ordinate analysis of similarity indices which were generated from binary data using both Dice and Jaccard coefficients. The analysis of binary DGGE data revealed significant impacts of N fertiliser on the eubacterial and actinomycete community structure using the Jaccard coefficient, whilst N fertiliser had a significant impact on the actinomycete community structure only when using similarity indices generated from the Dice coefficient. Soil drainage had a significant impact on the community structures of the actinomycetes and the pseudomonads using both Dice and Jaccard derived similarity indices. Multivariate analysis of principal components derived from PLFA profiling revealed that N fertiliser had a significant impact on the microbial community structure. Although drainage alone was not a significant factor in discriminating between PLFA community profiles of the different treatments, there was a significant interaction with N fertiliser. Analysis of principal component analysis (PCA) loadings revealed that PLFAs i15:0 and i17:0 were partly responsible for the clustering away of the undrained-N fertilised treatment. Although soil management regime influenced some background soil data, correlation analysis using PC1 from PLFA data revealed no significant relationship with soil organic matter, pH, total C and total N. These results provide evidence that grassland management practices impact on the community composition of specific microbial groups in soils.

Pressurized liquid extraction of soil microbial phospholipid and neutral lipid fatty acids

Soil microbial lipid biomarkers are indicators of viable microbial biomass and community structure. Pressurized liquid extraction (PLE) of soil phospholipid fatty acids (PLFA) and neutral lipid fatty acids (NLFA) was compared to a conventional extraction method in four soils with differing physical and chemical properties. PLE efficiency was greater than that of the conventional method for about half of the saturated PLFA and for selected other Gram-positive (i16:0) and Gram-negative bacteria (18:1omega7c) PLFA, fungal PLFA (18:2omega6,9c), and eukaryotic NLFA from a coarse-textured soil. Lipids extracted by the two methods did not indicate a significant difference in microbial community structure data. Principle component analysis revealed that PLFA clustered by location, with data indicating that the group of microbes contributing the greatest weight differed among soils. Overall, the PLE method proved to be more efficient at extracting soilborne microbial lipids while not altering microbial community information. These advantages indicate the PLE method is robust and well-suited to soil microbial ecology research.

Aboveground and belowground effects of single-tree removals in New Zealand rain forest

There has been considerable recent interest in how human-induced species loss affects community and ecosystem properties. These effects are particularly apparent when a commercially valuable species is harvested from an ecosystem, such as occurs through single-tree harvesting or selective logging of desired timber species in natural forests. In New Zealand mixed-species rain forests, single-tree harvesting of the emergent gymnosperm Dacrydium cupressinum, or rimu, has been widespread. This harvesting has been contentious in part because of possible ecological impacts of Dacrydium removal on the remainder of the forest, but many of these effects remain unexplored. We identified an area where an unintended 40-year "removal experiment" had been set up that involved selective extraction of individual Dacrydium trees. We measured aboveground and belowground variables at set distances from both individual live trees and stumps of trees harvested 40 years ago. Live trees had effects both above and below ground by affecting diversity and cover of several components of the vegetation (usually negatively), promoting soil C sequestration, enhancing ratios of soil C:P and N:P, and affecting community structure of soil microflora. These effects extended to 8 m from the tree base and were likely caused by poor-quality litter and humus produced by the trees. Measurements for the stumps revealed strong legacy effects of prior presence of trees on some properties (e.g., cover by understory herbs and ferns, soil C sequestration, soil C:P and N:P ratios), but not others (e.g., soil fungal biomass, soil N concentration). These results suggest that the legacy of prior presence of Dacrydium may remain for several decades or centuries, and certainly well over 40 years. They also demonstrate that, while large Dacrydium individuals (and their removal) may have important effects in their immediate proximity, within a forest, these effects should only be important in localized patches containing high densities of large trees. Finally, this study emphasizes that deliberate extraction of a particular tree species from a forest can exert influences both above and below ground if the removed species has a different functional role than that of the other plant species present.

Mesocosm-scale evaluation of faunal and microbial communities of aerated and unaerated leachfield soil

Aeration improves the capacity of leachfields to decontaminate and reduce the nutrient load of wastewater. To gain a better understanding of the effects of aeration, we examined the faunal and microbial communities of septic system leachfield soil (0-4 and 4-13 cm) using replicated (n = 3) mesocosms that were actively aerated (AIR) or unaerated (LEACH). Protozoa were 40 to 140 times more abundant in AIR than in LEACH soil. No nematodes were found in LEACH soil, whereas AIR soil contained 5 to 14 x 10(3) nematodes (all bacteriovores) kg(-1). Active microbial biomass was four to five times higher in AIR than LEACH soil. Proteobacteria and actinomycetes/sulfate-reducing bacteria constituted a higher proportion of the community in AIR soil, whereas anaerobic Gram-negative bacteria/firmicutes were more prominent in LEACH soil. Ratios of prokaryotic to eukaryotic phospholipid fatty acids (PLFAs) were higher in LEACH soil, as were membrane stress index values, whereas the starvation index was higher in AIR soil. Community-level physiological profiles showed that 29 and 30 different substrates were used for growth by LEACH and AIR soil microorganisms, respectively. The AIR soil had more microorganisms capable of growing on 10 substrates, whereas growth on two substrates was higher in LEACH soil. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA gene fragments revealed greater diversity of dominant phylotypes in AIR than LEACH soil, with communities separated by treatment. Aerated leachfield soil had a larger and more diverse faunal and microbial community than unaerated soil, possibly due to differences in the type and availability of electron acceptors.

Using phospholipid fatty acid technique to study short-term effects of the biological control agent Pseudomonas fluorescens DR54 on the microbial microbiota in barley rhizosphere

The biological control agent (BCA) Pseudomonas fluorescens DR54 was applied to seeds (experiment 1) or roots (experiment 2) of barley growing in microcosms, while noninoculated plants served as controls. The fate of the BCA and its effects on the rhizosphere microbial community was evaluated in microcosms destructively sampled at days 2, 4, 6, and 9 after inoculation. In both experiments the number of P. fluorescens DR54 cells decreased immediately after application as enumerated by immunostaining and microscope direct counting. Substrate-induced respiration (SIR) was taken as a measurement of the active microbial biomass, while indicators of the total microbiota (and main taxonomic groups) were obtained using the phospholipid fatty acid (PLFA) technique. In experiment 1, these parameters were unaffected by the relatively small number of BCA cells applied, whereas in experiment 2, the larger BCA input resulted in an enhanced level of both SIR and PLFAs from Gram-negative bacteria (which included the BCA itself). However, at day 9 after inoculation, treatments with P. fluorescens DR54 and controls were similar in all measured parameters in both experiments. This was also illustrated very clearly by principal component analysis of the PLFA data, which in both experiments were able to discriminate between treatments in the first days after BCA inoculation, thus confirming the sensitivity of this method. Laccase activity has a potential as an indicator of fungal stress, e.g., when challenged with an antifungal BCA. This seemed to be supported in experiment 2, where the activity of this enzyme was enhanced four-fold in the BCA treatment at day 2. Our study shows that under the present conditions, P. fluorescens DR54 disappears from the soil and causes only transient effects on the soil microbiota. It also shows that the PLFA technique is a sensitive and reliable monitoring tool in in situ assessment of BCA nontarget effect on indigenous microorganisms in soil.