Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.     

Phospholipid analysis as a tool to study complex microbial communities in marine sediments.

To complement information on microbial communities in marine sediments that can be obtained using microbiological methods, we developed an analytical procedure to trace microbial lipids in environmental samples. We focused on analyzing intact phospholipids as these membrane constituents are known to be biomarkers for viable cells. Analysis of intact phospholipids from a fractionated and preconcentrated sediment extract was achieved using liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). The combined analysis of phospholipid types and their fatty acid substituents allowed a differentiation between various groups of microorganisms living in the sediment. For comparison three strains of marine sulfate-reducing bacteria (SRB) were analysed for their lipid content.     

Microbial growth and resuscitation alter community structure after perturbation

Abstract: An increase in the number of culturable organisms and a decrease in the diversity of recoverable microbiota have been reported in deep subsurface materials after storage perturbation. The magnitude of the microbial community shift in stored samples was more pronounced at 4°C compared to −20°C. Phospholipid fatty acid analyses and acridine orange direct counts indicated that biomass did not increase significantly throughout storage. Changes in the types of fatty acid methyl esters determined over the time course indicated that some of the microbial community shift was due to bacterial proliferation. However, the recovery of new bacterial types only after the storage process suggested that some of the increase in culturable cell count was due to the resuscitation of dormant microorganisms, possibly activated by some aspect of sampling, sample handling, and/or storage. Comparison of acridine orange direct counts with phospholipid and diglyceride fatty acid content suggested that much of the biomass may have been non-living at early time points; however, after 30 days of storage most of the bacterial biomass was viable.     

Distribution and activity of microorganisms in subsurface sediments of a pristine study site in Oklahoma

Distribution and activity of microorganisms in surface soil and subsurface sediments were studied in depth profiles of six different microbial biomass and activity indicators (total direct counts, number of cells capable of electron transport system activity, viable cell plate counts, most Probable numbers of protozoa, and 4-hydroxybenzoate-degrading microorganisms, and ATP content). The profiles showed the same general trends on two different dates (January and June 1985). Seasonal variations were noted, but they were not extreme. Biomass and activity values declined sharply with depth in the unsaturated zone, reaching minima in a clay confining layer in the interface zone between 3 and 4 m. Contiguous 10-cm samples from the interface zone showed significant textural and microbiological variability. Higher and more stable biomass and activity values were detected in the saturated zone, the highest being a very permeable gravelly loamy sand layer at approximately 7.5 m. In this layer, viable counts were nearly equal to total counts and they approached the viable counts in surface soil. Surface-type protozoa and cyanobacteria also were detected in this layer, suggesting that it was connected hydrologically to a nearby river. Lowest values were detected in an underlying bedrock clay layer at 8 m, which, despite its impermeability and low viable counts, did contain measurable total counts, 4-hydroxybenzoate-degrading microorganisms, and ATP. Correlations were noted between sediment texture and microbial activity (i.e., sandy texture=high activity, clayey texture=low activity), but other hydrogeological and geochemical factors probably also influenced microbial distribution and activity in the profile.     

Microbial Community Growth and Utilization of Carbon Constituents During Thermophilic Composting at Different Oxygen Levels

Composting is characterized by dramatic changes in microbial community structure, to a high extent driven by changes in temperature and in the composition of the organic substrate. This study focuses on the interrelationships between decomposition of major classes in the organic material and dynamics in microbial populations during thermophilic composting of source-separated organic household waste. Experiments were performed in a 200-L laboratory reactor at 16, 2.5, and 1% O₂ in the compost atmosphere. Major classes of carbon constituents were analyzed by chemical methods, and the microbial biomass and community structure determined by fatty acid analyses with phospholipid fatty acids (PLFA) and total ester-linked fatty acids (EL) methods. At all three O₂ levels, the process was characterized by a rapid increase in microbial activity and biomass in the early thermophilic phase, although this period was delayed at the lower O₂ concentrations. Starch and fat were the main substrates utilized at all three O₂ levels during this period. The depletion of the starch fraction coincided with the beginning of a microbial biomass decrease, suggesting thatstarch is an important carbon substrate for the growth of thermophilic microorganisms during composting. Growth yields in the microbial community based on consumption of major carbon constituent classes in the high-activity period fell between 22 and 28%. Multivariate statistical analysis of changes in fatty acid composition revealed small, but statistically significant differences in the microbial community succession. At 16% O₂, 10Me fatty acids from Actinomycetes and cyclopropyl fatty acids (from Gram-negative bacteria) became more important with time, whereas 18:1ω7t was characteristic at 2.5 and 1% O₂, indicating a more stressed bacterial community at the lower O₂ concentrations. Although adequate composting was achieved at O₂ levels as low as 2.5 and 1%, it is not recommended to compost at such low levels in large-scale systems, because the heterogeneous gas transport through the material in these systems might lead to anaerobic conditions and inefficient composting.     

Spatial and Seasonal Variation in a Reservoir Sedimentary Microbial Community as Determined by Phospholipid Analysis

Sediment samples were collected monthly from Acton Lake, a eutrophic reservoir located in an agricultural region of southwestern Ohio, from three stations (River, Middle, and Dam) during the period May 1995 through January 1997. Sedimentary microbial biomass and community structures from these stations were studied using phospholipid analysis. At the River and Middle stations, the water column remained aerobic throughout the year, whereas the water overlying the Dam station sediments became anaerobic during summer stratification. Sedimentary microbial biomass at the River and Middle stations, as measured by the phospholipid phosphate (PLP) method, ranged from 225 to 450 nmol PLP g?1 d.w. (dry weight). Sedimentary microbial biomass at the Dam station was typically greater and ranged from 500 to 1,500 nmol PLP g?1 d.w. Principal component analysis of phospholipid fatty acid (PLFA) profiles indicated that the sedimentary microbial communities at all three stations displayed seasonal patterns of change. Among these patterns of change was a shift from aerobic microorganisms during times of cold water to anaerobic microorganisms during times of warm water. The Dam station differed from the River and Middle stations in that sediments from this station had disproportionately more polyenoic fatty acids, whereas sediments from the River and Middle stations had disproportionately more bacterial fatty acids. These data suggest that the Dam station may be a depositional zone for microeukaryotic phytoplankton produced in the overlying water column. These findings have implications for the understanding of carbon flux in reservoirs and preservation of organic matter in aquatic systems.     

Physiological Status and Community Composition of Microbial Mats of the Ebro Delta, Spain, by Signature Lipid Biomarkers

Abstract Physiological status of microbial mats of the Ebro Delta (Tarragona, Spain) based on the extraction of lipids considered ``signature lipid biomarkers' (SLB) from the cell membranes and walls of microorganisms has been analyzed. Data from a day–night cycle show significant differences in viable cells countings (PLFA cells counts) ranging from 1.5 × 10¹⁰ to 5.0 × 10¹⁰ cells g⁻¹ of sediment. Minimum values were observed at 18:00 and 6:00, when physicochemical conditions change drastically. The diversity of the microbial community was assessed by GC/MS analysis of phospholipid fatty acids (PLFA). The ratio of PLFA, representative of Gram-negative bacteria, comprises 47.8% of the total PLFA of the microbial mat community. The remaining PLFA was representative of Gram-positive (10.0%), anaerobic (5.7%), and eukaryotic microorganisms (5.7%), and other common lipids. Two different approaches were used as a comparative study to assess the physiological status of the microbial mats. Two parameters (cyclopropane fatty acids/ω7c monoenoic fatty acids, and measurement of the trans/cis monoenoic PLFA ratio) showed a minimum at midnight, suggesting the highest microbial activity. Higher values were observed at 18:00 and 6:00, coinciding with lower PLFA cell counts. Received: 14 May 1999; Accepted: 6 September 1999; Online Publication: 24 March 2000     

Biodegradation Processes in a Laboratory-Scale Groundwater Contaminant Plume Assessed by Fluorescence Imaging and Microbial Analysis

Flow reactors containing quartz sand colonized with biofilm were set up as physical model aquifers to allow degrading plumes of acetate or phenol to be formed from a point source. A noninvasive fluorescent tracer technique was combined with chemical and biological sampling in order to quantify transport and biodegradation processes. Chemical analysis of samples showed a substantial decrease in carbon concentration between the injection and outflow resulting primarily from dilution but also from biodegradation. Two-dimensional imaging of the aqueous oxygen [O₂(aq)] concentration field quantified the depletion of O₂(aq) within the contaminant plume and provided evidence for microbial respiration associated with biodegradation of the carbon source. Combined microbiological, chemical, and O₂(aq) imaging data indicated that biodegradation was greatest at the plume fringe. DNA profiles of bacterial communities were assessed by temperature gradient gel electrophoresis, which revealed that diversity was limited and that community changes observed depended on the carbon source used. Spatial variation in activity within the plume could be quantitatively accounted for by the changes observed in active cell numbers rather than differences in community structure, the total biomass present, or the increased enzyme activity of individual cells. Numerical simulations and comparisons with the experimental data were used to test conceptual models of plume processes. Results demonstrated that plume behavior was best described by growth and decay of active biomass as a single functional group of organisms represented by active cell counts.     

Heterotrophic Fixation of CO2 in Soil

The occurrence of heterotrophic CO₂ fixation by soil microorganisms was tested in several mineral soils differing in pH and two artificial soils (a mixture of silica sand, alfalfa powder, and nutrient medium inoculated with a soil suspension). Soils were incubated at ambient (∼0.05 vol%) and elevated (∼5 vol%) CO₂ concentrations under aerobic conditions for up to 21 days. CO₂ fixation was detected using either a technique for determining the natural abundance of ¹³C or by measuring the distribution of labeled ¹⁴C-CO₂ in soil and bacteria. The effects of elevated CO₂ on microbial biomass (direct counts, chloroform fumigation extraction method), composition of microbial community (phospholipid fatty acids), microbial activity (respiration, dehydrogenase activity), and turnover rate were also measured. Heterotrophic CO₂ fixation was proven in all soils under study, being higher in neutral soils. The main portion of the fixed CO₂ (98–99%) was found in extracellular metabolites while only ∼1% CO₂ was incorporated into microbial cells. High CO₂ concentration always induced an increase in microbial activity, changes in the composition of the microbial community, and a decrease in microbial turnover. The results suggest that heterotrophic CO₂ fixation could be a widespread process in soils.     

Microbial community structure and ecology of subglacial sediments in two polythermal Svalbard glaciers characterized by epifluorescence microscopy and PLFA

Biological and physico-chemical characteristics of subglacial sediments were studied in Svalbard. Sediment from close proglacial and supraglacial environments was used for a comparison. Viable bacteria, cyanobacteria and microalgae were detected in subglacial sediments from two polythermal glaciers using epifluorescence microscopy and phospholipid fatty acid (PLFA) analyses. The subglacial samples were generally of higher pH values, coarser texture and lower water content, organic matter, organic carbon, and nitrogen compared to proglacial and supraglacial sediments). Bacterial counts of 1.6 × 10⁷ cells mg^{− 1} OM (organic matter) were found. Cyanobacteria and algae were also of low abundance [4.2 cells mg^{− 1} DW (dry weight)]. Cyanobacteria comprised the major proportion of the autophotothrophic assemblages of subglacial soils. Deglaciated soils were similar to subglacial sediment in physico-chemical properties and microbial structure and numbers, unlike soil from vegetated sites or cryoconite sediment. In subglacial and deglaciated soil, relatively low diversity of microorganisms and low substrate availability was detected by PLFA analyses. Good accordance in microbial community structure assessments between epifluorescence microscopy and PLFA analyses was found. Our results suggest that the subglacial microbial populations can be divided into two groups: autochthonous microorganims (chemoheterotrophic bacteria) and allochthonous that retain the ability to proliferate and give rise to active population when conditions become favorable. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Lipid analysis of the response of a sedimentary microbial community to polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAH) are widespread environmental contaminants that can, under proper conditions, be degraded by microorganisms. The responses of a riverine sedimentary microbial community to PAH contamination were examined using an integrated biochemical assay that yielded data on PAH concentration, total microbial biomass, and microbial community structure and were interpreted using perturbation theory and the subsidy-stress gradient. Microbial mineralization of naphthalene, anthracene, fluorene, and phenanthrene was observed 24 h after their addition to all sediments sampled and ranged from 0.9 to 16.3% in ambient sediments and from 14.8 to 35.8% in contaminated sediments. Total microbial biomass, determined by phospholipid phosphate, increased in response to intermediate PAH concentration and decreased at sites with the highest PAH concentration (p < 0.05) during seven out of nine (78%) seasonal sampling periods. The two sampling periods that were not statistically different followed periods of high water and cold temperatures. Phospholipid fatty acid analysis of microbial community structure analysis indicated that increases in the relative abundance of gram-negative aerobes and heterotrophic eukaryotes were responsible, in part, for these observed increases in total microbial biomass. These findings (increased degradation rates, increased biomass at intermediate PAH concentrations, and altered community structure) indicate that a component of the microbial community responded to PAH as a usable input and are consistent with the predictions of perturbation theory and a subsidy-stress gradient.     

Fungal community composition and metabolism under elevated CO2 and O3

Atmospheric CO₂ and O₃ concentrations are increasing due to human activity and both trace gases have the potential to alter C cycling in forest ecosystems. Because soil microorganisms depend on plant litter as a source of energy for metabolism, changes in the amount or the biochemistry of plant litter produced under elevated CO₂ and O₃ could alter microbial community function and composition. Previously, we have observed that elevated CO₂ increased the microbial metabolism of cellulose and chitin, whereas elevated O₃ dampened this response. We hypothesized that this change in metabolism under CO₂ and O₃ enrichment would be accompanied by a concomitant change in fungal community composition. We tested our hypothesis at the free-air CO₂ and O₃ enrichment (FACE) experiment at Rhinelander, Wisconsin, in which Populus tremuloides, Betula papyrifera, and Acer saccharum were grown under factorial CO₂ and O₃ treatments. We employed extracellular enzyme analysis to assay microbial metabolism, phospholipid fatty acid (PLFA) analysis to determine changes in microbial community composition, and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) to analyze the fungal community composition. The activities of 1,4-β-glucosidase (+37%) and 1,4,-β-N-acetylglucosaminidase (+84%) were significantly increased under elevated CO₂, whereas 1,4-β-glucosidase activity (−25%) was significantly suppressed by elevated O₃. There was no significant main effect of elevated CO₂ or O₃ on fungal relative abundance, as measured by PLFA. We identified 39 fungal taxonomic units from soil using DGGE, and found that O₃ enrichment significantly altered fungal community composition. We conclude that fungal metabolism is altered under elevated CO₂ and O₃, and that there was a concomitant change in fungal community composition under elevated O₃. Thus, changes in plant inputs to soil under elevated CO₂ and O₃ can propagate through the microbial food web to alter the cycling of C in soil.     

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H₂, H₂S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.     

Carbon Source Utilization Profiles for Microbial Communities from Hydrologically Distinct Zones in a Basalt Aquifer

Abstract The Eastern Snake River Plain aquifer has hydrologically distinct zones in basalt flow units and interbedded sediments. The zones that differ markedly in physical features (e.g., porosity and permeability) have similar groundwater chemistries. The primary objective of this study was to determine whether intervals within the aquifer that contrast on the basis of permeability have distinct communities of unattached microorganisms based on functional attributes. Aquifer sampling was conducted using a submersible pump to obtain whole-well (w) samples, and a straddle-packer pump (SPP) to obtain samples from specific aquifer intervals that were vertically distributed in the open borehole. The SPP intervals ranged from 4.6 to 6.1 m in length and were located from 142 to 198 m below land surface. A community-level physiological profile (CLPP) was used to determine functional characteristics of the microbial community in the groundwater samples based on the community response to 95 sole organic carbon sources. Surface soil samples at the site were analyzed in a similar manner for comparison. The total bacterial population in the groundwater samples was determined using acridine orange direct counts. Principal components analysis (PCA) of the CLPP dataset distinguished between surface soil and aquifer microbial communities. Soils scored low in the respiration of polymers, esters, and amines and high in bromosuccinate, when compared to aquifer samples. The W samples were distinct from SPP samples. The 180- to 198-m interval, with the lowest hydraulic conductivity of all intervals, yielded samples that grouped together by PCA and cluster analysis. Direct counts varied between 10⁴ and 10⁵ cells ml⁻¹, and showed no relationship to the depth of the sample or to the hydraulic conductivity of the sample interval. Differences between microbial communities based on respired carbon compounds were discerned in separate, hydrologically distinct intervals within the borehole, although these differences were slight. Differences among aquifer intervals were less apparent than differences between surface soils and groundwater, and may be related to variations in hydrologic properties over the intervals sampled. The results suggest that free-living microbial communities in basalt aquifers, as characterized by CLPP are relatively unaffected by wide ranges in hydraulic conductivity when other abiotic factors are essentially equal. Received: 14 December 1995; Revised: 12 April 1996     

Microbial Communities in High and Low Recharge Environments: Implications for Microbial Transport in the Vadose Zone

Abstract Microbial communities along vertical transects in the unsaturated zone were evaluated at five sites in the Pasco Basin, in southeastern Washington State. Sites with contrasting recharge rates were chosen to maximize or minimize the potential for microbial transport. Pore water ages along the vertical transects were established using natural chloride tracers, and ranged from modern to either ∼15,000 yBP (years before present) or ∼30,000 yBP at the two low-recharge sites. Unsaturated flow processes were short-circuited by preferential flow at two of the three high-recharge sites, resulting in rapid movement of water through the vertical transects. Microbial numbers and biomass, based on plate counts, and phospholipid fatty acid (PLFA) concentrations decreased with depth at all sites. The majority (55–90%) of the culturable chemoheterotrophs recovered from most samples were streptomycete bacteria. 16S rRNA gene sequence and MIDI analyses indicated that 75% of the remaining isolates were Gram-positive bacteria (most likely species of Arthrobacter and Bacillus) 25% were Gram-negative bacteria (probably members of several genera in the alpha- and gamma-Proteobacteria). Comparison of microbial communities at low-recharge sites vs. high-recharge sites, where preferential flow occurs, revealed several differences that might be attributed to vertical transport of microbial cells at the high-recharge sites. Plate counts and PLFA analyses indicated that the proportion of streptomycetes, which were abundant at the surface but present in the subsurface as spores, decreased, or remained constant, with depth at the low-recharge sites, but increased with depth at the high-recharge sites. PLFA analyses also indicated that Gram-negative bacteria displayed increased nutrient stress with depth at the high-recharge sites characterized by preferential flow, but not at the low recharge site. This may be a result of advective transport of microbes to depths where it was difficult for them to compete effectively with the established community. Moreover, PLFA community structure profiles fluctuated considerably with depth at the low-recharge sites, but not at the high-recharge sites. This might be expected if transport were distributing the microbial community along the vertical profile at the high-recharge sites. In contrast to the high-recharge sites at which preferential flow occurs, filtration likely prevented vertical transport of microorganisms at the high-recharge site that was characterized by unsaturated flow. Received: 6 November 1996; Accepted: 9 May 1997     

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use

Abstract The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone. Received: 1 December 1999; Accepted: 6 June 2000; Online Publication: 28 August 2000     

Some special problems in the determination of viable counts of groundwater microorganisms

Factors affecting viable cell counts in groundwater or sediments were studied with samples from the Segeberg Forest test area in northern Germany. There was very little variation in results with the season (April, August, November) or depth of sampling; generally there were 10³–10⁴ aerobic cells per ml or g sediment. Long incubation times resulted in higher cell counts; groundwater samples required 4–5 weeks, and sediment extracts had to be cultured for 7 weeks. Total cell counts in sediment were 10²–10⁴ cell/g higher than viable cell counts of aerobes. This was explained partly by the additional presence of anaerobes and partly by the observation that some morphotypes may not have grown under our conditions. Viable cell counts were not influenced by cell extraction from the sediment with either Na-pyrophosphate or groundwater extracts. However, iron-precipitating or manganese-oxidizing bacteria were better extracted with sterile groundwater. The microflora of wells was more numerous than that of the free aquifer; consequently it was better to pump off all well water before aquifer water was sampled. The diameter of the well was also important; thinner tubes had higher cell counts than those with wider diameter. For sampling, wells should be at least 1 year old, since young wells contain higher numbers of microorganisms due to underground disturbances from the drilling. Turbid water samples could be clarified by filtration, but this reduced the viable counts by 1–2 orders of magnitude. Two different media inoculated with a sample dilution resulted in the same cell counts, but their microbial diversity was different. Storage of groundwater samples before processing resulted in up to 17-fold increases in cell counts and loss of diversity in the first 24 hours. Cell numbers decreased slowly during longer storage.     

Characterization of Microbial Consortia in Paddy Rice Soil by Phospholipid Analysis

Abstract Microbial biomass and community structure in paddy rice soil during the vegetation period of rice were estimated by analysis of their phospholipid fatty acids (PLFA), hydroxy fatty acids of lipopolysaccharides (LPS-HYFA), and phospholipid ether lipids (PLEL) directly extracted from the soil. A clear change in the composition of the community structure at different sampling periods was observed, indicated by the principal component analysis of the PLFA. A dramatic decline of ester-linked PLFA was observed in the soil samples taken at the second sampling time. In contrast to the ester-linked PLFA, the non-ester-linked PLFA composition did not change. The hydroxy fatty acids of lipopolysaccharides as well as ether lipids decreased consecutively during the observation period. Total microbial abundance was estimated to be (4.1–7.3) × 10⁹ cells g^-1 soil (dry weight). About 44% account for aerobic and 32% for facultative anaerobic bacteria, and 24% for archaea, on average. According to the profile and patterns of PLFA in the soil sample, it may be suggested that the paddy soil at the August sampling period contained more abundant facultative anaerobic bacteria (ca. 36%) and archaea (ca. 37%), but the total microbial biomass was significantly lower than in the remaining sampling periods. As the plant approached maturity, the microbial community structure in the soil changed to contain more abundant Gram-negative bacteria and methanotrophs. Received: 23 September 1999; Accepted: 28 February 2000; Online Publication: 12 May 2000     

Seasonal Variation in the Structure of a Marine Benthic Microbial Community

Abstract The patterns of seasonal variation in the structure of a marine benthic microbial community were examined using phospholipid fatty acid analysis (PLFA). Principal component analysis of PLFA profiles indicated a strong seasonal pattern dominated the variance within the data set. Three functional groups of microorganisms (phototrophic microeukaryotes, and two groups of anaerobic bacteria) were disproportionately abundant in the communities that mapped to either extreme of the first principle component. Phototrophic microeukaryotes were most abundant and exhibited the greatest relative abundance during periods of cold water. In contrast, the two functional groups of anaerobic bacteria showed the greatest relative abundance during times of warm water. Differential responses by these groups, and macrofaunal deposit feeders, to light intensity and water temperature were offered as the proximal causes of the observed patterns. Received: 28 April 1997; Accepted: 10 September 1997     

Barophilic Bacteria Associated with Digestive Tracts of Abyssal Holothurians

Abyssal holothurians and sediment samples were collected at depths of 4,430 to 4,850 m in the Demerara abyssal plain. Bacterial concentrations in progressive sections of the holothurian digestive tract, as well as in surrounding surface sediments, were determined by epifluorescence microscopy. Total bacterial counts in sediments recently ingested by the animals were 1.5- to 3-fold higher than in surrounding sediments at the deepest station. Lowest counts were observed consistently in the foregut, where the digestive processes of the holothurian are believed to occur. In most animals, counts increased 3- to 10-fold in the hindgut. Microbial activity at 3°C and in situ and atmospheric pressure were determined for gut and sediment samples by measuring the utilization of [¹⁴C]glutamic acid, the doubling time of the mixed-population of culturable bacteria, and the percentage of the total bacterial count responsive to yeast extract in the presence of nalidixic acid, using epifluorescence microscopy. A barophilic microbial population, showing elevated activity under deep-sea pressure, was detected by all three methods in sediments removed from the hindgut. Transmission electron micrographs revealed intact bacteria directly associated with the intestinal lining only in the hindgut. The bacteria are believed to be carried as an actively metabolizing, commensal gut flora that transforms organic matter present in abyssal sediments ingested by the holothurian. Using data obtained in this study, it was calculated that sediment containing organic matter altered by microbial activity cleared the holothurian gut every 16 h, suggesting that abyssal holothurians and their associated gut flora are important participants in nutrient cycles of the abyssal benthic ocean.