Diversity of microorganisms within rock varnish in the Whipple Mountains, California

Rock varnish from Arizona's Whipple Mountains harbors a microbial community containing about 10(8) microorganisms g(-1) of varnish. Analyses of varnish phospholipid fatty acids and rRNA gene libraries reveal a community comprised of mostly Proteobacteria but also including Actinobacteria, eukaryota, and a few members of the Archaea. Rock varnish represents a significant niche for microbial colonization.     

Community Structure Comparison Using FAME Analysis of Desert Varnish and Soil,Mojave Desert,California

While a number of studies have shown that a close association exists between microorganisms and varnished rocks, there is little hard evidence to support the existence of either specific desert varnish communities, or any role these microbes might play in the genesis of the varnish layers. To this end, we analyzed fatty acid methyl esters (FAMEs) of samples collected from the Mojave desert of southern California to compare the microbial community structure of desert varnish with the adjacent desert soil. These analyses indicated prokaryotic and fungal communities in both desert varnish and soil samples. FAMEs specific to gram-positive bacteria were found more often, and in greater abundance in varnish samples than in adjacent soils. This may represent a higher preservation potential of gram-positive bacteria fatty acids in varnish, a source area of varnish microorganisms dominated by gram-positive bacteria, or a varnish community dominated by gram-positive microorganisms. Heterogeneity in fatty acids was documented between varnished rocks and soils from different localities, as well as between samples collected from the same locality. This heterogeneity suggests that there are significant differences in the community structure of the microbial fauna found in varnish samples compared to the adjacent soil, and that desert varnish in the Mojave desert is not characterized by a unique and ubiquitous microbial community. These results suggest that the varnish is not a homogeneous and unique environment for biota, and provide no support for the hypothesis that the varnish layers are biogenic in origin.     

Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

A variety of microbially mediated metabolic pathways impact biogeochemical cycling in terrestrial subsurface environments. However, the role that viruses have in influencing microbial mortality and microbial community structure is poorly understood. Here we investigated the production of viruses and change in microbial community structure within shallow alluvial aquifer sediment slurries amended with ¹³C-labeled acetate and nitrate. Biostimulation resulted in production of viruses concurrent with acetate oxidation, ¹³CO₂ production and nitrate reduction. Interestingly, change in viral abundance was positively correlated to acetate consumption (r²=0.6252, P<0.05) and ¹³CO₂ production (r²=0.6572, P<0.05); whereas change in cell abundance was not correlated to acetate consumption or ¹³CO₂ production. Viral-mediated cell lysis has implications for microbial community structure. Betaproteobacteria predominated microbial community composition (62% of paired-end reads) upon inoculation but decreased in relative abundance and was negatively correlated to changes in viral abundance (r²=0.5036, P<0.05). As members of the Betaproteobacteria decreased, Gammaproteobacteria, specifically Pseudomonas spp., increased in relative abundance (82% of paired-end reads) and was positively correlated with the change in viral abundance (r²=0.5368, P<0.05). A nitrate-reducing bacterium, Pseudomonas sp. strain Alda10, was isolated from these sediments and produced viral-like particles with a filamentous morphology that did not result in cell lysis. Together, these results indicate that viruses are linked to carbon biogeochemistry and community structure in terrestrial subsurface sediments. The subsequent cell lysis has the potential to alter available carbon pools in subsurface environments, additionally controlling microbial community structure from the bottom-up.     

Cell-Specific Thioautotrophic Productivity of Epsilon-Proteobacterial Epibionts Associated with Shinkaia crosnieri

In this study, we report experimental evidence of the thioautotrophic activity of the epibiotic microbial community associated with the setae of Shinkaia crosnieri, a galatheid crab that is endemic to deep-sea hydrothermal systems in the Okinawa Trough in Japan. Microbial consumption of reduced sulfur compounds under in situ hydrostatic and atmospheric pressure provided evidence of sulfur-oxidizing activity by the epibiotic microbial community; the rate of sulfur oxidation was similar under in situ and decompressed conditions. Results of the microbial consumption of reduced sulfur compounds and tracer experiments using ¹³C-labeled bicarbonate in the presence and absence of thiosulfate (used as a thioautotrophic substrate) convincingly demonstrated that the epibiotic microbial community on S. crosnieri drove primary production via an energy metabolism that was coupled with the oxidation of reductive sulfur compounds. A combination of tracer experiments, fluorescence in situ hybridization (FISH) and nano-scale secondary ion mass spectrometry (Nano-SIMS) indicated that the filamentous cells of the genus Sulfurovum belonging to the class Epsilonproteobacteria were thioautotrophs in the epibiotic community of S. crosnieri. In conclusion, our results strongly suggest that thioautotrophic production by Sulfurovum members present as the epibiotic microbial community play a predominant role in a probable nutritional ectosymbiosis with S. crosnieri.     

Effect of Monospecific and Mixed Sea-Buckthorn (Hippophae rhamnoides) Plantations on the Structure and Activity of Soil Microbial Communities

This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH₄⁺) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram⁺ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH₄⁺ content, nitrate content (NH₃⁻), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations.     

Internal Tandem Duplication Mutations in FLT3 Gene Augment Chemotaxis to Cxcl12 Protein by Blocking the Down-regulation of the Rho-associated Kinase via the Cxcl12/Cxcr4 Signaling Axis

Internal tandem duplication mutations in the Flt3 gene (ITD-FLT3) enhance cell migration toward the chemokine Cxcl12, which is highly expressed in the therapy-protective bone marrow niche, providing a potential mechanism underlying the poor prognosis of ITD-FLT3⁺ acute myeloid leukemia. We aimed to investigate the mechanisms linking ITD-FLT3 to increased cell migration toward Cxcl12. Classification of the expression of Cxcl12-regulated genes in ITD-FLT3⁺ cells demonstrated that the enhanced migration of ITD-FLT3⁺ cells toward Cxcl12 was associated with the differential expression of genes downstream of Cxcl12/Cxcr4, which are functionally distinct from those expressed in ITD-FLT3⁻ cells but are independent of the Cxcr4 expression levels. Among these differentially regulated genes, the expression of Rock1 in the ITD-FLT3⁺ cells that migrated toward Cxcl12 was significantly higher than in ITD-FLT3⁻ cells that migrated toward Cxcl12. In ITD-FLT3⁻ cells, Rock1 expression and Mypt1 phosphorylation were transiently up-regulated but were subsequently down-regulated by Cxcl12. In contrast, the presence of ITD-FLT3 blocked the Cxcl12-induced down-regulation of Rock1 and early Mypt1 dephosphorylation. Likewise, the FLT3 ligand counteracted the Cxcl12-induced down-regulation of Rock1 in ITD-FLT3⁻ cells, which coincided with enhanced cell migration toward Cxcl12. Rock1 antagonists or Rock1 shRNA abolished the enhanced migration of ITD-FLT3⁺ cells toward Cxcl12. Our findings demonstrate that ITD-FLT3 increases cell migration toward Cxcl12 by antagonizing the down-regulation of Rock1 expression. These findings suggest that the aberrant modulation of Rock1 expression and activity induced by ITD-FLT3 may enhance acute myeloid leukemia cell chemotaxis to the therapy-protective bone marrow niche, where Cxcl12 is abundantly expressed.     

pH Influences the Distribution of Microbial Rock-Weathering Phenotypes in Weathered Shale Environments

Rock varnish is a darkly pigmented coating rich in manganese oxides. Though microbes inhabit varnish deposits, it is unclear whether they are involved in varnish formation. The fungal communities of rock varnish and adjacent rock sites with no visible varnish deposits were examined. Microcolonial fungi were identified at all sampling sites, and were associated with manganese oxides in patches of incipient varnish at non-varnish sites. Fungi were closely related to manganese-oxidizing genera and seventeen isolates oxidized manganese in culture, producing six distinct manganese-oxide morphologies. Our results indicate that microcolonial fungi may play a crucial role in rock varnish formation. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.     

Evaluation of Methyl Bromide Alternatives Efficacy against Soil-Borne Pathogens,Nematodes and Soil Microbial Community

Methyl bromide (MB) and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg^-1), methyl iodide (MI: 45.58 mg kg^-1), metham sodium (MS: 53.92 mg kg^-1) treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg^-1) and chloroform (CF: 23.68 mg kg^-1) showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.     

Effect of biofumigation and chemical fumigation on soil microbial community structure and control of pepper Phytophthora blight

Soil biofumigation with brassica plant residues has been shown to significantly suppress soilborne pathogen. However, little published data reported the impact of biofumigation on microbial community structure in pepper (Capsicum annuum L.) production systems under field conditions. Biofumigation with rapeseed (Brassica napus ‘Dwarf Essex’) meal and chemical fumigation with dazomet were tested to control the pepper disease caused by Phytophthora capsici. BF treatment showed the lowest disease incidence among these treatments. Effects on soil bacterial and fungal communities were assessed by denaturating gradient gel electrophoresis and the results showed that the biofumigation increased bacterial diversity and decreased fungal diversity. There was a negative correlation between soil bacterial diversity and disease incidence and a positive correlation between soil fungal diversity and disease incidence. Cloning of the microbial community showed that the microbial community structures were altered by biofumigation. Soil was also evaluated for their chemical properties. Biofumigation increased soil content of total N, NO₃ ^?–N, available P and available K. A significant correlation between soil microbial community structures and soil chemical properties was found. Overall, these results indicated that biofumigation reduced disease incidence of pepper through altering soil microbial community structures.     

The influence of goethite and gibbsite on soluble nutrient dynamics and microbial community composition

Iron and aluminum (oxyhydr)oxides are ubiquitous in the soil environment and have the potential to strongly affect the properties of dissolved organic matter. We examined the effect of oxide surfaces on soluble nutrient dynamics and microbial community composition using an incubation of forest floor material in the presence of (1) goethite and quartz, (2) gibbsite and quartz, and (3) quartz surfaces. Forest floor material was incubated over a period of 154 days. Aqueous extracts of the incubations were harvested on days 5, 10, 20, 30, 60, 90, and 154, and concentrations of P, N, PO₄ ^3?, NO₂ ^?, NO₃ ^?, and organic C were measured in the solutions. Microbial community composition was examined through pyrosequencing of bacterial and fungal small subunit ribosomal RNA genes on selected dates throughout the incubation. Results indicated that oxide surfaces exerted strong control on soluble nutrient dynamics and on the composition of the decomposer microbial community, while possibly having a small impact on system-level respiration. Goethite and gibbsite surfaces showed preferential adsorption of P-containing and high molar mass organic solutes, but not of N-containing compounds. On average, organic C concentrations were significantly lower in water extractable organic matter (WEOM) solutions from oxide treatments than from the control treatment (P = 0.0037). Microbial community composition varied both among treatments and with increasing time of incubation. Variation in bacterial and fungal community composition exhibited strong-to-moderate correlation with length of incubation, and several WEOM physiochemical characteristics including apparent (weight averaged) molar mass, pH and electrical conductivity. Additionally, variation in bacterial community composition among treatments was correlated with total P (r = 0.60, P < 0.0001), PO₄ ^3? (r = 0.79, P < 0.0001), and organic C (r = 0.36, P = 0.015) concentrations; while variation in fungal communities was correlated with organic C concentrations (r = ?0.48, P = 0.0008) but not with phosphorus concentrations. The relatively small impact of oxide surfaces on system-level microbial respiration of organic matter despite their significant effects on microbial community composition and WEOM dynamics lends additional support to the theory of microbial functional redundancy.     

To What Extent Do Food Preferences Explain the Trophic Position of Heterotrophic and Mixotrophic Microbial Consumers in a Sphagnum Peatland?

Although microorganisms are the primary drivers of biogeochemical cycles, the structure and functioning of microbial food webs are poorly studied. This is the case in Sphagnum peatlands, where microbial communities play a key role in the global carbon cycle. Here, we explored the structure of the microbial food web from a Sphagnum peatland by analyzing (1) the density and biomass of different microbial functional groups, (2) the natural stable isotope (δ ¹³C and δ ¹⁵N) signatures of key microbial consumers (testate amoebae), and (3) the digestive vacuole contents of Hyalosphenia papilio, the dominant testate amoeba species in our system. Our results showed that the feeding type of testate amoeba species (bacterivory, algivory, or both) translates into their trophic position as assessed by isotopic signatures. Our study further demonstrates, for H. papilio, the energetic benefits of mixotrophy when the density of its preferential prey is low. Overall, our results show that testate amoebae occupy different trophic levels within the microbial food web, depending on their feeding behavior, the density of their food resources, and their metabolism (i.e., mixotrophy vs. heterotrophy). Combined analyses of predation, community structure, and stable isotopes now allow the structure of microbial food webs to be more completely described, which should lead to improved models of microbial community function.     

Microbial community development in the traps of aquatic Utricularia species

We examined trap fluid of three aquatic carnivorous species of Utricularia (Lentibulariaceae) to assess the role of microbial community within their traps in plant nutrient acquisition. In the context of increasing trap age, we characterized microbial community composition using phospholipid fatty acid (PLFA) analysis and microscopy. Nutrient content in various fractions of the trap fluid was analyzed and the abundance of free-suspended bacteria estimated. The activities of extracellular phosphatase in the trap fluid were determined using fluorometry and the contribution of the microbial community to phosphatase production assessed by epifluorescence microscopy. The trap microbial community seems to be largely derived from Utricularia associated periphyton. PLFA analysis revealed that trap fluid contained all components of a complex microbial food web with bacteria forming more than 58% of the viable microbial biomass in the trap. Trap age seems to be the key factor in determining the patterns of microbial community development as well as enzyme production. The amount of nutrients increases with increasing trap age, and the total amounts of C, N, and P accumulated within traps during their lifetime are relatively large—of the order of 100 mg L⁻¹ for C and N, and between 0.2 and 0.6 mg L⁻¹ for P. A significant part of the nutrient pool is present in the dissolved form. Trap fluid stoichiometry (molar N:P ratios about 100) as well as the presence of nutrient limited microbial cells (molar N:P ratios 25–61) indicates the importance of phosphorus rather than nitrogen for the nutrition of Utricularia. Our findings support the hypothesis that mutualism, apart from the predator–prey interaction, is an important association in aquatic Utricularia traps and that the trap-associated microbial community may be of benefit to the rootless aquatic Utricularia species facing problems with P acquisition due to the loss of roots in their evolution.     

Aerobic decolorization of Acid Brilliant Scarlet GR by microbial community and the community dynamics during sequencing batch processes

In this research, aerobic decolorization of Acid Brilliant Scarlet GR by microbial community was studied. Effects of conditions and dye concentraion on decolorization processes were investigated. Additionally, continuous decolorization was evaluated through sequencing batch tests and the microbial dynamics during this process was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis. The results showed that 100 mg l^?1 of the dye was completely decolorized within 12 h, which was mainly caused by biodegradation. The optimal decolorization conditions were as follows: inoculation size 2.07 g l^?1 (wet cell pellet), rotation speed 150 r min^?1, pH 5.0–7.0 and 30 °C. The processes were well described by zero-order kinetics, and more than 700 mg l^?1 of the dye would inhibit the activity of the consortium. Furthermore, the microbial community exhibited high efficiency in sequencing batch processes for continuous decolorization. Microbial community structure shifted obviously when exposed to higher concentration of the dye (500 mg l^?1), and all the dominant microorganisms were affiliated with four different phyla of Actinobacteria, Bacteroidetes, Proteobacteria and Firmicutes.     

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia,China

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12–267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO₄^2-, SO₄^2-/total sulfur ratio, and Fe²⁺ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.     

Microbial biomass,respiration and diversity in ultramafic soils of West Dome,New Zealand

Ultramafic soils are colonised by plant communities adapted to naturally elevated heavy metal content but it is not known whether soil microbial communities are similarly adapted to heavy metals. We measured microbial properties of six ultramafic soils that ranged in heavy metal content to test whether microbial diversity would decrease and respiratory quotient (microbial respiration:biomass) increase due to the stress imposed by increasing metal content. Soil samples were collected from beneath Nothofagus solandri var. cliffortioides tall forest, tall Leptospermum scoparium shrubland, open Leptospermum scoparium shrubland, an open Leptospermum scoparium shrubland with the rare ultramafic endemic Celmisia spedenii, a mixed divaricate shrubland, and a red tussock (Chionochloa rubra) grassland on the Dun Mountain Ophiolite belt, New Zealand. Samples were analysed for catabolic evenness using the catabolic response profile technique, microbial biomass, microbial respiration, and soil properties (pH, total carbon, total nitrogen, magnesium and total or extractable chromium and nickel). The sites differed in base saturation, pH and concentrations of metals, particularly magnesium, chromium and nickel, properties that are a major determinant of the plant communities that develop. Microbial biomass and respiration, catabolic evenness (range of 19.1 to 22.7) and the respiratory quotient were not correlated to any of the measured soil chemical properties. Factor analysis of the respiratory responses showed that the microbial communities under each vegetation type were distinct. The second factor extracted was correlated to total carbon (r ²=0.62, P<0.01), basal respiration (r ²=0.55, P<0.01) and microbial biomass (r ²=0.65, P<0.01). Increasing metals concentrations had no direct impact on microbial diversity, biomass, respiration or community energetics. However, we suggest that metal concentrations may have exerted an indirect effect on the structure of the microbial communities through control of the vegetation community and litter inputs of carbon to the soil.     

Linking microbial community structure to membrane biofouling associated with varying dissolved oxygen concentrations

In order to elucidate how dissolved oxygen (DO) concentration influenced the generation of extracellular polymeric substance (EPS) and soluble microbial products (SMP) in mixed liquor and biocake, 16S rDNA fingerprinting analyses were performed to investigate the variation of the microbial community in an aerobic membrane bioreactor (MBR). The function of microbial community structure was proved to be ultimately responsible for biofouling. Obvious microbial community succession from the subphylum of Betaproteobacteria to Deltaproteobacteria was observed in biocake. High concentration of EPS in biocake under the low DO concentration (0.5 mg L⁻¹) caused severe biofouling. The correlation coefficient of membrane fouling rate with EPS content in biocake (0.9941-0.9964) was much higher than that in mixed liquor (0.6689-0.8004).     

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r² = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r² = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r² = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.     

Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy

Ecosystems have a limited buffering capacity of multiple ecosystem functions against biodiversity loss (i.e. low multifunctional redundancy). We developed a novel theoretical approach to evaluate multifunctional redundancy in a microbial community using the microbial genome database (MBGD) for comparative analysis. In order to fully implement functional information, we defined orthologue richness in a community, each of which is a functionally conservative evolutionary unit in genomes, as an index of community multifunctionality (MF). We constructed a graph of expected orthologue richness in a community (MF) as a function of species richness (SR), fit the power function to SR (i.e. MF = cSR^a), and interpreted the higher exponent a as the lower multifunctional redundancy. Through a microcosm experiment, we confirmed that MF defined by orthologue richness could predict the actual multiple functions. We simulated random and non-random community assemblages using full genomic data of 478 prokaryotic species in the MBGD, and determined that the exponent in microbial communities ranged from 0.55 to 0.75. This exponent range provided a quantitative estimate that a 6.6–8.9% loss limit in SR occurred in a microbial community for an MF reduction no greater than 5%, suggesting a non-negligible initial loss effect of microbial diversity on MF.     

Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magna carcasses and ¹³C-labelled maize leaves (Zea mays) were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). ¹³C stable-isotope measurements of CO₂ analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C–N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.Subject terms: Limnology, Biogeochemistry, Ecology, Microbiology     

Soil microbial community structure in European forests in relation to forest type and atmospheric nitrogen deposition

The objective of the present study was to evaluate the combined effect of vegetation and N deposition on microbial community composition in forest soils. For this, microbial biomass and community structure were assessed by ester linked fatty acid methyl ester (EL-FAME) analyses for 12 European forest sites representing different forest types (coniferous/deciduous) and differing in annual N loads (2?C40 kg?N?ha^?1). Microbial community composition was affected by vegetation as indicated by a higher proportion of the marker for arbuscular mycorrhiza (AM) fungi??16:1 11???in deciduous forest soils (1.2%?C5.7% of total EL-FAMEs) compared to acidic coniferous forest soils (0.5%?C1.6%). The two pine forest sites investigated showed the highest proportion of fungi (up to 28% of total EL-FAMEs) and the lowest proportions of Gram-negative and Gram-positive bacteria of all study sites. Nitrogen deposition rates were highly correlated with the ratios of cyclopropyl fatty acids to their precursors (r?=?0.82; P?<?0.01) and of bacteria to fungi (r?=?0.71; P?<?0.05). The two sites with the highest N deposition (??32.3 kg?N?ha^?1a^?1) were depleted in the marker fatty acids for AM fungi and other fungi. Our findings suggest that vegetation has a pronounced effect on microbial community structure, but this effect is masked by high N inputs (>30 kg?N?ha^?1a^?1).