Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate.     

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation

Endophytes are ubiquitous plant‐associated microbes and although they have the potential to alter the decomposition of infected leaf litter, this has not been well‐studied. The endophyte Rhytisma punctatum infects the leaves of Acer macrophyllum (bigleaf maple), causing the appearance of black ‘tar spots’ that persist in senesced leaves. Other foliar fungi also cause visible damage in healthy tissues of this host plant system including an unidentified bullseye‐shaped lesion, common in western Washington. Using three treatments of endophyte infection status in leaf tissue (R. punctatum‐infected, bullseye‐infected, lesion‐free), leaf litter discs were submerged in a third‐order temperate stream using mesh litter bags and harvested periodically over two months to determine the effects of litter treatment and incubation time on litter mass loss, fungal sporulation, and microbial community colonization. Litter containing symptomatic endophyte infections (Rhytisma or bullseye) had reduced sporulation of aquatic hyphomycetes, but decomposed significantly faster than lesion‐free or bullseye‐infected litter. Using amplicon‐based sequencing, we found a significant difference in bacterial communities colonizing Rhytisma‐infected and bullseye‐infected leaf litter, a significant difference in fungal communities colonizing Rhytisma‐infected leaf litter compared to the two other treatments, and a change in both community structure and relative abundances of bacterial and fungal taxa throughout the study period. Indicator Species Analysis clarified the drivers of these community shifts at the genus level. Our results show that endophyte‐associated, in‐stream sporulation and microbial community effects are observable within one species of leaf litter.     

Increasing Red Maple Leaf Litter Alters Decomposition Rates and Nitrogen Cycling in Historically Oak-Dominated Forests of the Eastern U.S.

Without canopy-opening fire disturbances, shade-tolerant, fire-sensitive species like red maple (Acer rubrum L.) proliferate in many historically oak-dominated forests of the eastern U.S. Here, we evaluate potential implications of increased red maple dominance in upland oak forests of Kentucky on rates of leaf litter decomposition and nitrogen (N) cycling. Over 5 years, we evaluated mass loss of leaf litter and changes in total N and carbon (C) within six leaf litter treatments comprised of scarlet oak, chestnut oak, and red maple, and three mixed treatments of increasing red maple contribution to the leaf litter pool (25, 50, and 75% red maple). Over a 1.5-year period, we conducted a plot-level leaf litter manipulation study using the same treatments plus a control and assessed changes in net nitrification, ammonification, and N mineralization within leaf litter and upper (0–5 cm depth) mineral soil horizons. Red maple leaf litter contained more “fast” decomposing material and initially lost mass faster than either oak species. All litter treatments immobilized N during initial stages of decomposition, but the degree of immobilization decreased with decreasing red maple contribution. The leaf litter plot-level experiment confirmed slower N mineralization rates for red maple only plots compared to chestnut oak plots. As red maple increases, initial leaf litter decomposition rates will increase, leading to lower fuel loads and more N immobilization from the surrounding environment. These changes may reduce forest flammability and resource availability and promote red maple expansion and thereby the “mesophication” of eastern forests of the U.S.     

Riparian plant species loss alters trophic dynamics in detritus-based stream ecosystems

Riparian vegetation is closely connected to stream food webs through input of leaf detritus as a primary energy supply, and therefore, any alteration of plant diversity may influence aquatic ecosystem functioning. We measured leaf litter breakdown rate and associated biological parameters in mesh bags in eight headwater streams bordered either with mixed deciduous forest or with beech forest. The variety of leaf litter types in mixed forest results in higher food quality for large-particle invertebrate detritivores (‘shredders’) than in beech forest, which is dominated by a single leaf species of low quality. Breakdown rate of low quality (oak) leaf litter in coarse mesh bags was lower in beech forest streams than in mixed forest streams, a consequence of lower shredder biomass. In contrast, high quality (alder) leaf litter broke down at similar rates in both stream categories as a result of similar shredder biomass in coarse mesh bags. Microbial breakdown rate of oak and alder leaves, determined in fine mesh bags, did not differ between the stream categories. We found however aquatic hyphomycete species richness on leaf litter to positively co-vary with riparian plant species richness. Fungal species richness may enhance leaf litter breakdown rate through positive effects on resource quality for shredders. A feeding experiment established a positive relationship between fungal species richness per se and leaf litter consumption rate by an amphipod shredder (Gammarus fossarum). Our results show therefore that plant species richness may indirectly govern ecosystem functioning through complex trophic interactions. Integrating microbial diversity and trophic dynamics would considerably improve the prediction of the consequences of species loss.     

Diversity of Fungi, Bacteria, and Actinomycetes on Leaves Decomposing in a Stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.     

Diversity of fungi, bacteria, and actinomycetes on leaves decomposing in a stream

Although fungi, bacteria, and specific bacterial taxa, such as the actinomycetes, have been studied extensively in various habitats, few studies have examined them simultaneously, especially on decomposing leaves in streams. In this study, sugar maple and white oak leaves were incubated in a stream in northeastern Ohio for 181 days during which samples were collected at regular intervals. Following DNA extraction, PCR-denaturing gradient gel electrophoresis (DGGE) was performed using fungus-, bacterium-, and actinomycete-specific primers. In addition, fungal and bacterial biomass was estimated. Fungal biomass differed on different days but not between leaves of the two species and was always greater than bacterial biomass. There were significant differences in bacterial biomass through time and between leaf types on some days. Generally, on the basis of DGGE, few differences in community structure were found for different leaf types. However, the ribotype richness of fungi was significantly greater than those of the bacteria and actinomycetes, which were similar to each other. Ribotype richness decreased toward the end of the study for each group except bacteria. Lack of differences between the two leaf types suggests that the microorganisms colonizing the leaf biofilm were primarily generalists that could exploit the resources of the leaves of either species equally well. Thus, we conclude that factors, such as the ecological role of the taxa (generalists versus specialists), stage of decay, and time of exposure, appeared to be more important determinants of microbial community structure than leaf quality.     

Characterization of Humus Microbial Communities in Adjacent Forest Types That Differ in Nitrogen Availability

To address the link between soil microbial community composition and soil processes, we investigated the microbial communities in forest floors of two forest types that differ substantially in nitrogen availability. Cedar-hemlock (CH) and hemlock-amabilis fir (HA) forests are both common on northern Vancouver Island, B.C., occurring adjacently across the landscape. CH forest floors have low nitrogen availability and HA high nitrogen availability. Total microbial biomass was assessed using chloroform fumigation-extraction and community composition was assessed using several cultivation-independent approaches: denaturing gradient gel electrophoresis (DGGE) of the bacterial communities, ribosomal intergenic spacer analysis (RISA) of the bacterial and fungal communities, and phospholipid fatty acid (PLFA) profiles of the whole microbial community. We did not detect differences in the bacterial communities of each forest type using DGGE and RISA, but differences in the fungal communities were detected using RISA. PLFA analysis detected subtle differences in overall composition of the microbial community between the forest types, as well as in particular groups of organisms. Fungal PLFAs were more abundant in the nitrogen-poor CH forests. Bacteria were proportionally more abundant in HA forests than CH in the lower humus layer, and Gram-positive bacteria were proportionally more abundant in HA forests irrespective of layer. Bacterial and fungal communities were distinct in the F, upper humus, and lower humus layers of the forest floor and total biomass decreased in deeper layers. These results indicate that there are distinct patterns in forest floor microbial community composition at the landscape scale, which may be important for understanding nutrient availability to forest vegetation.     

Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass

Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the α-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the α-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate “4clt”).     

Fungal communities on decaying leaves in streams: a comparison of two leaf species

Decomposition of leaf litter is a microbial mediated process that helps to transfer energy and nutrients from leaves to higher trophic levels in woodland streams. Generally, aquatic hyphomycetes are viewed as the major fungal group responsible for leaf litter decomposition. In this study, traditional microscopic examination (based on identification of released conidia) and phylogenetic analysis of 18S rRNA genes from cultivated fungi were used to compare fungal community composition on decomposing leaves of two species (sugar maple and white oak) from a NE Ohio stream. No significant differences were found in sporulation rates between maple and oak leaves and both had similar species diversity. From the 18S rRNA gene sequence data, identification was achieved for 12 isolates and taxonomic affiliation of 12 of the remaining 14 isolates could be obtained. A neighbor-joining tree (with bootstrap values) was constructed to examine the taxonomic distribution of the isolates relative to sequences of known operational taxonomic units (OTUs). Surprisingly, only 2 of the isolates obtained were aquatic hyphomycetes based on phylogenetic analysis. Overall, there were no differences between the two leaf types and a higher diversity was observed via culturing and subsequent 18S rRNA gene sequencing than by conidia staining. These differences resulted from the fact that traditional microscopy provides estimates of aquatic hyphomycete diversity while the other approach revealed the presence of both aquatic hyphomycete and non-aquatic hyphomycete taxa. The presence of this broad array of taxa suggests that the role of aquatic hyphomycetes relative to other fungi be re-evaluated. Even though the functional role of these non-aquatic hyphomycetes taxa is unknown, their presence and diversity demonstrates the need to delve further into fungal community structure on decomposing leaves.     

Red oak litter promotes a microarthropod functional group that accelerates its decomposition

The contribution of microarthropod activity to litter decomposition varies widely but can be substantial. Oribatid mites are the most diverse and abundant of the microarthropod groups in forest litter. This experiment was designed to examine the effect of litter type and complexity on the diversity and species composition of oribatid mites, and to test whether alterations in species composition due to litter type affected litter decomposition. In an array of plots on a mixed-hardwood site in the mountains of North Carolina, I exposed microarthropod assemblages to a range of litter types: yellow birch, sugar maple, red oak and two mixed litters. Over several years, the litter types selected oribatid mite assemblages of different species composition. By comparing the decomposition of consecutive cohorts of litter, it was possible to detect differences in decomposition accompanying the shifts in the assemblage. A comparison of the mass loss rates between the two litter cohorts over eighteen months reveals similar trajectories for four litter types. In the oak litter, however, the second cohort disappeared significantly faster than the first. In both years, the litters came from the same trees and were nearly identical in initial carbon and nitrogen contents. Since the response was specific to oak litter, it is unlikely that differences in environmental factors are responsible for the faster mass loss of oak. A significant increase of endophagous oribatid mites, those that burrow into plant material, in the second cohort of oak may account for its accelerated decomposition. The woody petioles and thick leaf-planes of oak leaves provide microhabitats for burrowing mites. Endophage activity can accelerate the litter decomposition both through direct comminution of leaf material and by facilitating microbial growth. Because of their low population growth rates, oribatid populations that are reduced by disturbance are slow to recover and by disrupting these non-resilient populations, disturbance may have long-term repercussions for decomposition. This revised version was published online in June 2006 with corrections to the Cover Date.     

Effect of Inorganic Nutrients on Relative Contributions of Fungi and Bacteria to Carbon Flow from Submerged Decomposing Leaf Litter

The relative contributions of fungi and bacteria to carbon flow from submerged decaying plant litter at different levels of inorganic nutrients (N and P) were studied. We estimated leaf mass loss, fungal and bacterial biomass and production, and microbial respiration and constructed partial carbon budgets for red maple leaf disks precolonized in a stream and then incubated in laboratory microcosms at two levels of nutrients. Patterns of carbon flow for leaf disks colonized with the full microbial assemblage were compared with those colonized by bacteria but in which fungi were greatly reduced by placing leaf disks in colonization chambers sealed with membrane filters to exclude aquatic hyphomycete conidia but not bacterial cells. On leaves colonized by the full microbial assemblage, elevated nutrient concentrations stimulated fungi and bacteria to a similar degree. Peak fungal and bacterial biomass increased by factors of 3.9 and 4.0; cumulative production was 3.9 and 5.1 times higher in the high nutrient in comparison with the low nutrient treatment, respectively. Fungi dominated the total microbial biomass (98.4 to 99.8%) and cumulative production (97.3 and 96.5%), and the fungal yield coefficient exceeded that of bacteria by a factor of 36 and 27 in low- and high-nutrient treatments, respectively. Consequently, the dominant role of fungi in leaf decomposition did not change as a result of nutrient manipulation. Carbon budgets indicated that 8% of leaf carbon loss in the low-nutrient treatment and 17% in the high-nutrient treatment were channeled to microbial (essentially fungal) production. Nutrient enrichment had a positive effect on rate of leaf decomposition only in microcosms with full microbial assemblages. In treatments where fungal colonization was reduced, cumulative bacterial production did not change significantly at either nutrient level and leaf decomposition rate was negatively affected (high nutrients), suggesting that bacterial participation in carbon flow from decaying leaf litter is low regardless of the presence of fungi and nutrient availability. Moreover, 1.5 and 2.3 times higher yield coefficients of bacteria in the reduced fungal treatments at low and high nutrients, respectively (percentage of leaf carbon loss channeled to bacterial production), suggest that bacteria are subjected to strong competition with fungi for resources available in leaf litter.     

Distinct Bacterial Communities Dominate Tropical and Temperate Zone Leaf Litter

Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic “plant beneficial” lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.     

Microbial Community Structure and Oxidative Enzyme Activity in Nitrogen-amended North Temperate Forest Soils

Large regions of temperate forest are subject to elevated atmospheric nitrogen (N) deposition which can affect soil organic matter dynamics by altering mass loss rates, soil respiration, and dissolved organic matter production. At present there is no general model that links these responses to changes in the organization and operation of microbial decomposer communities. Toward that end, we studied the response of litter and soil microbial communities to high levels of N amendment (30 and 80 kg ha^–1 yr^–1) in three types of northern temperate forest: sugar maple/basswood (SMBW), sugar maple/red oak (SMRO), and white oak/black oak (WOBO). We measured the activity of extracellular enzymes (EEA) involved directly in the oxidation of lignin and humus (phenol oxidase, peroxidase), and indirectly, through the production of hydrogen peroxide (glucose oxidase, glyoxal oxidase). Community composition was analyzed by extracting and quantifying phospholipid fatty acids (PLFA) from soils. Litter EEA responses at SMBW sites diverged from those at oak-bearing sites (SMRO, BOWO), but the changes were not statistically significant. For soil, EEA responses were consistent across forests types: phenol oxidase and peroxidase activities declined as a function of N dose (33–73% and 5–41%, respectively, depending on forest type); glucose oxidase and glyoxal oxidase activities increased (200–400% and 150–300%, respectively, depending on forest type). Principal component analysis (PCA) ordinated forest types and treatment responses along two axes; factor 1 (44% of variance) was associated with phenol oxidase and peroxidase activities, factor 2 (31%) with glucose oxidase. Microbial biomass did not respond to N treatment, but nine of the 23 PLFA that formed >1 mol% of total biomass showed statistically significant treatment responses. PCA ordinated forest types and treatment responses along three axes (36%, 26%, 12% of variance). EEA factors 1 and 2 correlated negatively with PLFA factor 1 (r = –0.20 and –0.35, respectively, n = 108) and positively with PLFA factor 3 (r = +0.36 and +0.20, respectively, n = 108). In general, EEA responses were more strongly tied to changes in bacterial PLFA than to changes in fungal PLFA. Collectively, our data suggests that N inhibition of oxidative activity involves more than the repression of ligninase expression by white-rot basidiomycetes.This revised version was published online in November 2004 with corrections to Volume 48.     

Microbial Population Changes during Bioremediation of an Experimental Oil Spill

Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.     

Differential effects of sugar maple, red oak, and hemlock tannins on carbon and nitrogen cycling in temperate forest soils

Tannins are abundant secondary chemicals in leaf litter that are hypothesized to slow the rate of soil-N cycling by binding protein into recalcitrant polyphenol–protein complexes (PPCs). We studied the effects of tannins purified from sugar maple, red oak, and eastern hemlock leaf litter on microbial activity and N cycling in soils from northern hardwood–conifer forests of the northeastern US. To create ecologically relevant conditions, we applied tannins to soil at a concentration (up to 2 mg g⁻¹ soil) typical of mineral soil horizons. Sugar maple tannins increased microbial respiration significantly more than red oak or hemlock tannins. The addition of sugar maple tannins also decreased gross N mineralization by 130% and, depending upon the rate of application, decreased net rates of N mineralization by 50–290%. At low concentrations, the decrease in mineralization appeared to be driven by greater microbial-N immobilization, while at higher concentrations the decrease in mineralization was consistent with the formation of recalcitrant PPCs. Low concentrations of red oak and hemlock tannins stimulated microbial respiration only slightly, and did not significantly affect fluxes of inorganic N in the soil. When applied to soils containing elevated levels of protein, red oak and hemlock tannins decreased N mineralization without affecting rates of microbial respiration, suggesting that PPC formation decreased substrate availability for microbial immobilization. Our results indicate that tannins from all three species form recalcitrant PPCs, but that the degree of PPC formation and its attendant effect on soil-N cycling depends on tannin concentration and the pool size of available protein in the soil.     

Effects of consumers and nitrogen availability on heterotrophic microbial activity during leaf decomposition in headwater streams

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Molecular Analysis of Diazotroph Diversity in the Rhizosphere of the Smooth Cordgrass, Spartina alterniflora

N₂ fixation by diazotrophic bacteria associated with the roots of the smooth cordgrass, Spartina alterniflora, is an important source of new nitrogen in many salt marsh ecosystems. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are unknown. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified nifH sequence segments was used in previous studies to examine the stability and dynamics of the Spartina rhizosphere diazotroph assemblages in the North Inlet salt marsh, near Georgetown, S.C. In this study, plugs were taken from gel bands from representative DGGE gels, the nifH amplimers were recovered and cloned, and their sequences were determined. A total of 59 sequences were recovered, and the amino acid sequences predicted from them were aligned with sequences from known and unknown diazotrophs in order to determine the types of organisms present in the Spartina rhizosphere. We recovered numerous sequences from diazotrophs in the γ subdivision of the division Proteobacteria (γ-Proteobacteria) and from various anaerobic diazotrophs. Diazotrophs in the α-Proteobacteria were poorly represented. None of the Spartina rhizosphere DGGE band sequences were identical to any known or previously recovered environmental nifH sequences. The Spartina rhizosphere diazotroph assemblage is very diverse and apparently consists mainly of unknown organisms.     

Phylogenetic Composition of Arctic Ocean Archaeal Assemblages and Comparison with Antarctic Assemblages

Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota.     

Comparison of characterization and microbial communities in rice straw- and wheat straw-based compost for <Emphasis Type="Italic">Agaricus bisporus</Emphasis> production

Rice straw (RS) is an important raw material for the preparation of Agaricus bisporus compost in China. In this study, the characterization of composting process from RS and wheat straw (WS) was compared for mushroom production. The results showed that the temperature in RS compost increased rapidly compared with WS compost, and the carbon (C)/nitrogen (N) ratio decreased quickly. The microbial changes during the Phase I and Phase II composting process were monitored using denaturing gradient gel electrophoresis (DGGE) and phospholipid fatty acid (PLFA) analysis. Bacteria were the dominant species during the process of composting and the bacterial community structure dramatically changed during heap composting according to the DGGE results. The bacterial community diversity of RS compost was abundant compared with WS compost at stages 4–5, but no distinct difference was observed after the controlled tunnel Phase II process. The total amount of PLFAs of RS compost, as an indicator of microbial biomass, was higher than that of WS. Clustering by DGGE and principal component analysis of the PLFA compositions revealed that there were differences in both the microbial population and community structure between RS- and WS-based composts. Our data indicated that composting of RS resulted in improved degradation and assimilation of breakdown products by A. bisporus, and suggested that the RS compost was effective for sustaining A. bisporus mushroom growth as well as conventional WS compost.     

Linking the Physicochemical Properties with the Abundance and Diversity of Rhizospheric Bacterial Population Inhabiting Paddy Soil Based on a Concerted Multivariate Analysis of PCR-DGGE and RISA

To unravel the existence of dominant bacterial population in the paddy fields of Eastern Uttar Pradesh, India and their relation to the prevailing soil physicochemistry using multivariate statistical analyses, a cumulative culture-independent 16S rRNA based Polymerase chain reaction-Denaturing gradient gel electrophoresis (PCR-DGGE) and a 16S-23S ribosomal intergenic spacer analysis (RISA) have been performed. Detrended correspondence analysis (DCA) and principal component analysis (PCA) biplot analyses were used to assess the relation between soil bacterial population and its physicochemistry. DCA analysis exhibited a strong dependence of bacterial existence on the soil physicochemical variables, such as organic matter, total nitrogen, inorganic nutrients, temperatures, and moisture status. Soil dehydrogenase activity (DHA) was assessed to check the metabolic activity of all soil samples which showed a range of 0.012–0.050 nmol TPF g^?1 min^?1 with significant variation (p < 0.01). Out of 96 bands excised, 45 different phylotypes were obtained using both techniques which elucidated the abundance of Cyanobacteria over other soil bacterial population. Scytonema sp., Leptolyngbya sp. and different uncultured cyanobacterial species were the major genera found. Profiling data obtained through PCR-DGGE and RISA were used in alpha diversity and rarefaction curve analysis suggested site 6 (Chandauli) as the most diversity rich site. Thus extensive dataset of weighted and unweighted variables generated through DGGE and RISA coupled with metabolic functioning of soil and multivariate analyses provided an excellent opportunity to map the soil microbial structure in paddy fields and their regulation with existing soil environment.