Soil microbial community characteristics along an elevation gradient in the Laguna Mountains of Southern California

We sampled soil at four sites in the Laguna Mountains in the western Sonoran Desert to test the effects of site and sample location (between or beneath plants) on fatty acid methyl ester (FAME) and carbon substrate ulilization (Biolog) profiles. The four sites differed in elevation, soil type, plant community composition, and plant percent cover. Soil pH decreased and plant density increased with elevation. Fertile islands, defined as areas beneath plants with greater soil resources than bare areas, are present at all sites, but are most pronounced at lower elevations. Consistent with this pattern, fertile islands had the greatest influence on FAME and Biolog profiles at lower elevations. Based on the use of FAME biomarker and principal components analyses, we found that soil microbial communities between plants at the lowest elevation had proportionally more Gram-negative bacteria than all other soils. At the higher elevation sites there were few differences in FAME profiles of soils sampled between vs. beneath plants. Differences in FAME profiles under plants among the four sites were small, suggesting that the plant influence per se is more important than plant type in controlling FAME profiles. Since microbial biomass carbon was correlated with FAME number (r=0.85,P<0.0001) and with FAME named (r=0.88,P<0.0001) and total areas (r=0.84,P<0.0001), we standardized the FAME data to ensure that differences in FAME profiles among samples were not the result of differences in microbial biomass. Differences in microbial substrate utilization profiles among sampling locations were greatest between samples taken under vs. between plants at the two lower elevation sites. Microbial substrate utilization profiles, therefore, also seem to be influenced more by the presence of plants than by specific plant type.     

Microbial activity and leaching during initial oak leaf litter decomposition

The decomposition of oak leaf litter was studied by means of a litterbag experiment in an oak forest in the Netherlands. The contribution of microbial activity and leaching to weight loss and element dynamics during the first 6 weeks of decomposition was investigated by means of frequent respiration measurements and extractions of the litter and by a qualitative comparison of throughfall and litter percolation water chemistry. The oak-leaf litter lost 9.3% of its initial dry weight during the first 6 weeks. In total, 90% of this observed weight loss was explained by the processes studied. About 5.9% (64% of the total) of this weight loss was attributed to microbial tespiration and 0.5% (5%) to the loss of inorganic solutes. Leaching of dissolved organic compounds was estimated to account for 2.0% (21%). The results indicated a fast leaching of K and Cl out of the fresh litter during the first 2 weeks, while Mg, Fe, Mn, Si, ortho P, and dissolved organic N were released at a much lower rate. At the same time, small amounts of H⁺, NH _inf4 ^sup+ and NO _inf3 ^sup- were retained in the litter.     

The problem of pretreatment and unintentional variations in the fumigation-extraction method for time-course measurements in the field

A control soil stored at 4°C was analyzed 38 times by fumigation-extraction during a period of 11 months to correct for variations caused by the analytical procedure. The difference in extractable C between fumigated and unfumigated samples oscillated around the average without a positive or negative trend. When data from contemporaneously extracted field samples were corrected with control soil data the variations were lowered. The deviations between corrected and uncorrected biomass C values had maxima of ±12%. Data obtained for seven dates using pre-extraction, wet-sieving, and centrifuging were compared with data obtained by the conventional procedure without any pretreatment. A negative difference from data obtained without pretreatment was found when the soil water content was decreased to 6%. The largest positive difference (+38%) was found in May during the period of highest root growth.     

Growth of the collembolan Folsomia candida Willem in soil supplemented with glucose

Freely available glucose improves the conditions for soil microorganisms which are utilized as food by Collembola. We examined the effects of glucose application on collembolan (Folsomia candida Willem) growth and on several biotic and abiotic soil parameters (microbial biomass, soil respiration, qCO₂, dissolved organic carbon, inorganic nitrogen, and Olson-P) in an artificial system without predatory pressure on Collembola. Glucose addition increased soil respiration and qCO₂, and decreased nutrient levels in the soil. Collembolan growth increased with increasing glucose doses. We conclude that the availability of carbon substrates can sustain collembolan growth via an improvement of microbial growth conditions.     

Organic matter status and the size, activity and metabolic diversity of the soil microbial community in the row and inter-row of sugarcane under burning and trash retention

The concentrations of organic C, labile organic fractions and the size and activity of the microbial community were measured to a depth of 30 cm below the plant row and at distances of 30 and 60 cm into the inter-row area under sugarcane under pre-harvest burning or green cane harvesting with retention of a crop residue (trash) mulch. Total root mass was similar under burning and trashing but under trashing there was a redistribution of roots towards the surface 0-10 cm in the inter-row space as roots proliferated beneath the trash mulch. Soil organic C content decreased in response to both increasing distance from the plant row (to a depth of 20 cm) and burning rather than trashing (to a depth of 10 cm). Declines in K₂SO₄-extractable C, light fraction C, microbial biomass C, basal respiration and aggregate stability in response to distance and burning were much more marked than those for organic C and occurred to a depth of 30 cm. Bulk density was greater under burnt than trashed sugarcane and was greater in the inter-row than row, particularly under burning. Heterotrophic functional diversity (measured by analysis of catabolic response profiles to 36 substrates) was also investigated. Principal component analysis of response profiles demonstrated that soils below the row and those under trashing at 30 cm out from this row were separated from the other soils on PC1 and the sample from the inter-row centre (60 cm out) under burning was separated from the others on PC2. Catabolic evenness was least for the latter soil. It was concluded that soil in the inter-row of burnt sugarcane receives few inputs of organic matter and that conversion to green cane harvesting with retention of a trash mulch greatly improves the organic matter, microbial and physical status of the inter-row soil.     

Soil microbial and nutrient dynamics in a wet Arctic sedge meadow in late winter and early spring

Microbial activity is known to continue during the winter months in cold alpine and Arctic soils often resulting in high microbial biomass. Complex soil nutrient dynamics characterize the transition when soil temperatures approach and exceed 0 °C in spring. At the time of this transition in alphine soils microbial biomass declines dramatically together with soil pools of available nutrients. This pattern of change characterizes alpine soils at the winter-spring transition but whether a similar pattern occurs in Arctic soils, which are colder, is unclear. In this study amounts of microbial biomass and the availability of carbon (C), nitrogen (N) and phosphorus (P) for microbial and plant growth in wet peaty soils of an Arctic sedge meadow have been determined across the winter-spring boundary. The objective was to determine the likely causes of the decline in microbial biomass in relation to temperature change and nutrient availability. The pattern of soil temperature at depths of 5-15 cm can be divided into three phases: below −10 °C in late winter, from −7 to 0 °C for 7 weeks during a period of freeze-thaw cycles and above 0 °C in early spring. Peak microbial biomass and nutrient availability occurred early in the freeze-thaw phase. Subsequently, a steady decrease in inorganic N occurred, so that when soil temperatures rose above 0 °C, pools of inorganic nutrients in soils were very low. In contrast, amounts of microbial C and soluble organic C and N remained high until the end of the period of freeze-thaw cycles, when a sudden collapse occurred in soluble organic C and N and in phosphatase activity, followed by a crash in microbial biomass just prior to soil temperatures rising consistently above 0 °C. Following this, there was no large pulse of available nutrients, implying that competition for nutrients from roots results in the collapse of the microbial pool.     

Multivariate effects of plant canopy, soil physico-chemistry and microbiology on Sclerotinia stem rot of soybean in relation to crop rotation and urban compost amendment

The effects of canopy, soil physico-chemical and microbiological variables on Sclerotinia stem rot (SSR) on soybean were assessed in two soils (clay loam and sandy loam) using multiple regression and canonical redundancy analysis (RDA) and their partial form to control for the rotation (2 or 3-y-corn/soybean monoculture) and fertilization (mineral/urban compost) or spatial variables effects. The models revealed the minimal sets of variables that best explain the variance of the survival of Sclerotinia sclerotiorum’s sclerotia, carpogenic germination, disease severity and their associations. In clay loam, the 3-y-corn rotation reduced disease severity mainly through the reduction of weed biomass that favoured carpogenic germination. Urban compost has a conducive effect explained by a better soil surface drainage. Additionally, total N was found suppressive to sclerotial survival. In sandy loam, the carpogenic germination was negatively correlated with high C mineralization quotient and aggregate stability but correlated positively with Ca. Sclerotial survival was negatively correlated with pH and Ca, and positively correlated with biological fertility index. Aggregate stability, Ca and pH were associated with the urban compost. The regression and RDA analyses allowed to identify key variables that drived SSR development and explain their relationship with the cultural practices, soil health, as well as the spatial variation of disease variables.     

Developments in soil microbiology since the mid 1960s

Since the 1960s, soil microbiology underwent major changes in methods and approaches and this review focuses on the developments in some selected aspects of soil microbiology. Research in cell numbers of specific bacterial and fungal groups was replaced by a focus on biochemical processes including soil enzyme activities, and flux measurements of carbon and nutrients. Ecologists focused on soil microbial pools whereas soil microbial biomass as an important source and sink of nutrients were recognized in agriculture. Soil microbiologists started to use structural components like phospholipid fatty acids for quantification of specific microbial groups without the need to cultivate them. In the last decade, molecular approaches allowed new insights through the analysis of soil extract DNA showing an unexpected diversity of genomes in soil. At the end of the review a brief outlook is given on the future of soil microbiology which ranges from in situ identification of bacteria, to routine assays of microbial communities by microarray technology.     

Microbial dynamics in an anaerobic soil slurry amended with glucose, and their dependence on geochemical processes

Under anoxic conditions, microbial activities interact closely with geochemical reactions and consequently affect soils, underlying aquifers, and the atmosphere. Recent studies have noted the relationships between microbial biodiversity and environmental conditions, but the dynamics of numerous coexisting microbial groups in connection with soil biogeochemical processes has never been investigated. In this work, we investigated the dynamics of anaerobic microbial populations using a new method combining PCR-SSCP and epifluorescent direct counts, and analysed these results in the light of biogeochemical changes. Batch incubations were performed over an 8-day period on a calcic cambisol (WRB) incubated anaerobically, either without amendment (treatment C) or after adding glucose (treatment +G). In treatment +G, the predominant microbial processes included (i) NO₃⁻ and NO₂⁻ reduction during the first 12 and 24 h of incubation respectively, (ii) fermentations during the first 6 days with non-symbiotic N₂ fixation between days 1 and 6, enabling bacterial growth during this period, and probably (iii) reduction of FeIII by H₂ oxidation throughout the incubation period. In treatment C, microbiological and geochemical measurements revealed no prominent microbial activities, and the PCR-SSCP method led to complex bacterial density profiles without prominent peaks. In treatment +G, 78 microbial groups were distinguished; these were divided into seven sets (A to G) according to their dynamics. Bacteria belonging to sets A, E and F grew during the period of intense fermentation and were probably able to fix N₂, as is the case with Clostridium butyricum (set A). Bacteria belonging to sets B, D, and G were probably able to reduce FeIII to FeII with concomitant oxidation of H₂ into H₃O⁺, but unable to fix N₂. Two microbial groups in these sets were closely related to Clostridium favosporum (set B) and the genus Bacillus (set B). Bacteria belonging to class C were probably only able to reduce N oxide(s). Lastly, we obtained two similar estimates of the gross increase in microbial biomass by taking into account either (i) the sum of gross increases for the 78 microbial groups, or (ii) the energy yield of catabolic reactions minus the energy requirement for N₂ fixation.     

Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies

Microbial digestive enzymes in soil and litter have been studied for over a half century, yet the understanding of microbial enzymes as drivers of ecosystem processes remains hindered by methodological differences among researchers and laboratories. Modern techniques enable the comparison of enzyme activities from different sites and experiments, but most researchers do not optimize enzyme assay methods for their study sites, and thus may not properly assay potential enzyme activity. In this review, we characterize important procedural details of enzyme assays, and define the steps necessary to properly assay potential enzyme activities in environmental samples. We make the following recommendations to investigators measuring soil enzyme activities: 1) run enzyme assays at the environmental pH and temperature; 2) run proper standards, and if using fluorescent substrates with NaOH addition, use a standard time of 1 min between the addition of NaOH and reading in a fluorometer; 3) run enzyme assays under saturating substrate concentrations to ensure V_max is being measured; 4) confirm that product is produced linearly over the duration of the assay; 5) examine whether mixing during the reaction is necessary to properly measure enzyme activity; 6) find the balance between dilution of soil homogenate and assay variation; and 7) ensure that enzyme activity values are properly calculated. These steps should help develop a unified understanding of enzyme activities in ecosystem ecology.