Low Bacterial Biomass Research Articles

Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines.

When studying the microbiome using next-generation sequencing, the DNA extraction method, sequencing procedures, and bioinformatic processing are crucial to obtain reliable data. Method choice has been demonstrated to strongly affect the final biological interpretation. We assessed the performance of three DNA extraction methods and two bioinformatic pipelines for bacterial microbiota profiling through 16S rRNA gene amplicon sequencing, using positive and negative controls for DNA extraction and sequencing and eight different types of high- or low-biomass samples. Performance was evaluated based on quality control passing, DNA yield, richness, diversity, and compositional profiles. All DNA extraction methods retrieved the theoretical relative bacterial abundance with a maximum 3-fold change, although differences were seen between methods, and library preparation and sequencing induced little variation. Bioinformatic pipelines showed different results for observed richness, but diversity and compositional profiles were comparable. DNA extraction methods were successful for feces and oral swabs, and variation induced by DNA extraction methods was lower than intersubject (biological) variation. For low-biomass samples, a mixture of genera present in negative controls and sample-specific genera, possibly representing biological signal, were observed. We conclude that the tested bioinformatic pipelines perform equally, with pipeline-specific advantages and disadvantages. Two out of three extraction methods performed equally well, while one method was less accurate regarding retrieval of compositional profiles. Lastly, we again demonstrate the importance of including negative controls when analyzing low-bacterial-biomass samples.IMPORTANCE Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to contribute to increased methodological consistency in microbiota studies. Our methods were applied not only to commonly studied samples for microbiota analysis, e.g., feces, but also to more rarely studied, low-biomass samples. Microbiota composition profiles of low-biomass samples (e.g., urine and tumor biopsy specimens) were not always distinguishable from negative controls, or showed partial overlap, confirming the importance of including negative controls in microbiota studies, especially when low bacterial biomass is expected.

A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males

OBJECTIVETo determine if urinary microbial communities similar to those described in adults exist in children and to profile the urinary and gastrointestinal microbiome in children presenting to urology for both routine and complex urologic procedures. METHODSPrepubertal boys (n = 20, ages 3 months-8 years; median age 15 months) who required elective urologic procedures were eligible. Urine samples were collected via sterile catheterization and fecal samples were obtained by rectal swabs. DNA was extracted from urine pellet and fecal samples and subjected to bacterial profiling via 16S rDNA Illumina sequencing and 16S rDNA quantitative polymerase chain reaction. We assessed within and between sample diversity and differential species abundance between samples. RESULTSUrine samples had low bacterial biomass that reflected the presence of bacterial populations. The most abundant genera detected in urine samples are not common to skin microbiota and several of the genera have been previously identified in the urinary microbiome of adults. We report presumably atypical compositional differences in both the urinary and gastrointestinal microbiome in children with prior antibiotic exposure and highlight an important case of a child who had undergone lifelong antibiotic treatment as prophylaxis for congenital abnormalities. CONCLUSIONThis study provides one of the first characterizations of the urinary microbiome in prepubertal males. Defining the baseline healthy microbiome in children may lay the foundation for understanding the long-term impact of factors such as antibiotic use in the development of a healthy microbiome as well as the development of future urologic and gastrointestinal diseases.

Microbial generation of elemental mercury from dissolved methylmercury in seawater.

Elemental mercury (Hg0) formation from other mercury species in seawater results from photoreduction and microbial activity, leading to possible evasion from seawater to overlying air. Microbial conversion of monomethylmercury (MeHg) to Hg0 in seawater remains unquantified. A rapid radioassay method was developed using gamma-emitting 203Hg as a tracer to evaluate Hg0 production from Hg(II) and MeHg in the low pM range. Bacterioplankton assemblages in Atlantic surface seawater and Long Island Sound water were found to rapidly produce Hg0, with production rate constants being directly related to bacterial biomass and independent of dissolved Hg(II) and MeHg concentrations. About 32% of Hg(II) and 19% of MeHg were converted to Hg0 in 4 d in Atlantic surface seawater containing low bacterial biomass, and in Long Island Sound water with higher bacterial biomass, 54% of Hg(II) and 8% of MeHg were transformed to Hg0. Decreasing temperatures from 24°C to 4°C reduced Hg0 production rates cell-1 from Hg(II) 3.3 times as much as from a MeHg source. Because Hg0 production rates were linearly related to microbial biomass and temperature, and microbial mercuric reductase was detected in our field samples, we inferred that microbial metabolic activities and enzymatic reactions primarily govern Hg0 formation in subsurface waters where light penetration is diminished.

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

BackgroundMost of our knowledge about the remarkable microbial diversity on Earth comes from sequencing the 16S rRNA gene. The use of next-generation sequencing methods has increased sample number and sequencing depth, but the read length of the most widely used sequencing platforms today is quite short, requiring the researcher to choose a subset of the gene to sequence (typically 16–33% of the total length). Thus, many bacteria may share the same amplified region, and the resolution of profiling is inherently limited. Platforms that offer ultra-long read lengths, whole genome shotgun sequencing approaches, and computational frameworks formerly suggested by us and by others all allow different ways to circumvent this problem yet suffer various shortcomings. There is a need for a simple and low-cost 16S rRNA gene-based profiling approach that harnesses the short read length to provide a much larger coverage of the gene to allow for high resolution, even in harsh conditions of low bacterial biomass and fragmented DNA.ResultsThis manuscript suggests Short MUltiple Regions Framework (SMURF), a method to combine sequencing results from different PCR-amplified regions to provide one coherent profiling. The de facto amplicon length is the total length of all amplified regions, thus providing much higher resolution compared to current techniques. Computationally, the method solves a convex optimization problem that allows extremely fast reconstruction and requires only moderate memory. We demonstrate the increase in resolution by in silico simulations and by profiling two mock mixtures and real-world biological samples. Reanalyzing a mock mixture from the Human Microbiome Project achieved about twofold improvement in resolution when combing two independent regions. Using a custom set of six primer pairs spanning about 1200 bp (80%) of the 16S rRNA gene, we were able to achieve ~ 100-fold improvement in resolution compared to a single region, over a mock mixture of common human gut bacterial isolates. Finally, the profiling of a Drosophila melanogaster microbiome using the set of six primer pairs provided a ~ 100-fold increase in resolution and thus enabling efficient downstream analysis.ConclusionsSMURF enables the identification of near full-length 16S rRNA gene sequences in microbial communities, having resolution superior compared to current techniques. It may be applied to standard sample preparation protocols with very little modifications. SMURF also paves the way to high-resolution profiling of low-biomass and fragmented DNA, e.g., in the case of formalin-fixed and paraffin-embedded samples, fossil-derived DNA, or DNA exposed to other degrading conditions. The approach is not restricted to combining amplicons of the 16S rRNA gene and may be applied to any set of amplicons, e.g., in multilocus sequence typing (MLST).

Uptake of dissolved organic and inorganic nitrogen in microalgae-dominated sediment: comparing dark and light in situ and ex situ additions of 15N

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 571:29-42 (2017) - DOI: https://doi.org/10.3354/meps12127 Uptake of dissolved organic and inorganic nitrogen in microalgae-dominated sediment: comparing dark and light in situ and ex situ additions of 15N Philip M. Riekenberg*, Joanne M. Oakes, Bradley D. Eyre Centre for Coastal Biogeochemistry, Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia *Corresponding author: phrieken@gmail.com ABSTRACT: Microbial communities within bare intertidal sediment have an active role in uptake of inorganic and organic nitrogen as it is transported through estuaries. 15N-labeled dissolved inorganic nitrogen (DIN, NH4+; 250 µmol l-1, 500 µmol l-1) and dissolved organic nitrogen (DON, algal-derived; 125 µmol l-1, 250 µmol l-1) were applied to diatom-dominated sandy intertidal sediment under light and dark conditions to investigate short-term N uptake (24 h). Two experiments compared uptake in intact sediments (in situ) and homogenized slurries (ex situ). In both experiments, N uptake was similar in light and dark conditions, and benthic microalgae (BMA) dominated both biomass and DIN and DON uptake over heterotrophic bacteria. Substantially lower uptake of DON than DIN occurred for both experiments, likely because organic molecules require extracellular processing before uptake by BMA. Compared to intact sediments, sediment slurries had higher N uptake into sediment organic matter (3-36×), lower bacterial biomass (13.6 ± 3.5% versus 41.1 ± 7.6% intact) and low bacterial contribution to 15N uptake (14 ± 0.8% versus 14 ± 3.0%). Differences are likely due to shifts within the microbial community and sediment environment caused by sediment homogenization or incubation effects. Consistently, uptake rates within slurries were greater than within intact sediments, and patterns of significant differences among treatments were different. Slurry incubations are therefore not reliable for quantification or comparison of in situ uptake rates across different N substrates, but biomarkers appear robust between the 2 methods, indicating low bacterial contribution to N uptake in BMA-dominated sediment. KEY WORDS: Benthic microalgae · Bacteria · Microphytobenthos · DON · DIN · Slurry · Stable isotope Full text in pdf format Supplementary material PreviousNextCite this article as: Riekenberg PM, Oakes JM, Eyre BD (2017) Uptake of dissolved organic and inorganic nitrogen in microalgae-dominated sediment: comparing dark and light in situ and ex situ additions of 15N. Mar Ecol Prog Ser 571:29-42. https://doi.org/10.3354/meps12127 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 571. Online publication date: May 17, 2017 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2017 Inter-Research.

Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform

BackgroundThe composition of the skin microbiome is predicted to play a role in the development of conditions such as atopic eczema and psoriasis. 16S rRNA gene sequencing allows the investigation of bacterial microbiota. A significant challenge in this field is development of cost effective high throughput methodologies for the robust interrogation of the skin microbiota, where biomass is low. Here we describe validation of methodologies for 16S rRNA (ribosomal ribonucleic acid) gene sequencing from the skin microbiome, using the Illumina MiSeq platform, the selection of primer to amplify regions for sequencing and we compare results with the current standard protocols..MethodsDNA was obtained from two low density mock communities of 11 diverse bacterial strains (with and without human DNA supplementation) and from swabs taken from the skin of healthy volunteers. This was amplified using primer pairs covering hypervariable regions of the 16S rRNA gene: primers 63F and 519R (V1-V3); and 347F and 803R (V3-V4). The resultant libraries were indexed for the MiSeq and Roche454 and sequenced. Both data sets were denoised, cleaned of chimeras and analysed using QIIME.ResultsThere was no significant difference in the diversity indices at the phylum and the genus level observed between the platforms. The capture of diversity using the low density mock community samples demonstrated that the primer pair spanning the V3-V4 hypervariable region had better capture when compared to the primer pair for the V1-V3 region and was robust to spiking with human DNA. The pilot data generated using the V3-V4 region from the skin of healthy volunteers was consistent with these results, even at the genus level (Staphylococcus, Propionibacterium, Corynebacterium, Paracoccus, Micrococcus, Enhydrobacter and Deinococcus identified at similar abundances on both platforms).ConclusionsThe results suggest that the bacterial community diversity captured using the V3-V4 16S rRNA hypervariable region from sequencing using the MiSeq platform is comparable to the Roche454 GS Junior platform. These findings provide evidence that the optimised method can be used in human clinical samples of low bacterial biomass such as the investigation of the skin microbiota.

Efficacy of acetate-amended biostimulation for uranium sequestration: Combined analysis of sediment/groundwater geochemistry and bacterial community structure

Systematic flow-through column experiments were conducted using sediments and ground water collected from different subsurface localities at the U.S. Department of Energy's Integrated Field Research Challenge site in Rifle, Colorado. The principal purpose of this study is to gain a better understanding of the interactive effects of groundwater geochemistry, sediment mineralogy, and indigenous bacterial community structures on the efficacy of uranium removal from the groundwater with/without acetate amendment. Overall, we find that the subtle variations in the sediments' mineralogy, redox conditions, as well as contents of metal(loid) co-contaminants showed a pronounced effect on the associated bacterial population and composition, which mainly determines the system's performance with respect to uranium removal. Positive relationship was identified between the abundance of dissimilatory sulfate-reduction genes (i.e., drsA), markers of sulfate-reducing bacteria, and the sediments' propensity to sequester aqueous uranium. In contrast, no obvious connections were observed between the abundance of common iron-reducing bacteria, e.g., Geobacter spp., and the sediments' ability to sequester uranium. In the sediments with low bacterial biomass and the absence of sulfate-reducing conditions, abiotic adsorption onto mineral surfaces such as phyllosilicates likely played a relatively major role in the attenuation of aqueous uranium; however, in these scenarios, acetate amendment induced detectable rebounds in the effluent uranium concentrations. The results of this study suggest that immobilization of uranium can be achieved under predominantly sulfate-reducing conditions, and provide insight into the integrated roles of various biogeochemical components in long-term uranium sequestration.

Partitioning of wastewater treatment high rate algal pond biomass and particulate carbon

The partitioning of algae, bacteria, grazers and detritus in two wastewater treatment high rate algal ponds (HRAPs) was investigated in relation to particulate carbon (PC) over a year. Algae dominated the pond biomass accounting for ~61% of the PC. Changes in algal biomass correlated with changes in PC with both varying seasonally and having spring or summer maxima. The algal biomass itself was dominated by larger cells or colonies in the 20–200μm size fraction with Pediastrum sp. prominent. Bacterial biomass, in contrast, only accounted for ~13.5% of the PC and varied less seasonally. Grazer biomass was lowest at ~4% of the PC on average and was dominated by either zooplankton or microzooplankton. Grazer biomass however, varied the most and reached ~14% of the PC during a spring zooplankton bloom that markedly reduced algal biomass. The remaining ~21.5% of the PC was made up of dead algal, detrital matter, and mucilage that tended to aggregated into bio-floccs. The PC of an efficiently operating HRAP is shown to be driven by high algal biomass with low bacterial and grazer biomass. If this balance is lost grazers may grow to levels that enable them to reduce algal biomass and productivity compounding pond instability.

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples.

BackgroundThe advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications.ResultsWe herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation. When compared to previous reports, we identified an additional 88 bacterial genera as potential contaminants of molecular biology grade reagents, bringing the total number of known contaminating microbes to 181 genera. Many of the contaminants detected are considered normal inhabitants of the human gastrointestinal tract and the environment and are often indistinguishable from those genuinely present in the sample.ConclusionsLaboratories working on bacterial populations need to define contaminants present in all extraction kits and reagents used in the processing of DNA. Any unusual and/or unexpected findings need to be viewed as possible contamination as opposed to unique findings.Electronic supplementary materialThe online version of this article (doi:10.1186/s13099-016-0103-7) contains supplementary material, which is available to authorized users.

Stimulation of soil microorganisms in pesticide-contaminated soil using organic materials

Agrochemicals such as pesticides have contributed to significant increases in crop yields; however, they can also be linked to adverse effects on human health and soil microorganisms. For efficient bioremediation of pesticides accumulated in agricultural fields, stimulation of microorganisms is necessary. In this study, we investigated the relationships between bacterial biomass and total carbon (TC) and total nitrogen (TN) in 427 agricultural soils. The soil bacterial biomass was generally positively correlated with TC and TN contents in the soil, but some soils had a low bacterial biomass despite containing high amounts of TC and TN. Soils of two fields (fields A and B) with low bacterial biomass but high TC and TN contents were investigated. Long-term pesticide use (dichloropropane-dichloropropene and fosthiazate in field A and chloropicrin in field B) appeared to have contributed to the low bacterial biomass observed in these soils. Soil from field A was treated with different organic materials and incubated for 1 month under laboratory conditions. The bacterial biomass in field A soil was enhanced in treatments containing organic materials rich in TN. Application of organic materials stimulated the growth of microorganisms with the potential to bioremediate pesticide-polluted soils.

Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA

Microbial metagenomics are hindered in clinical tissue samples as a result of the large relative amount of human DNA in relation to microbial DNA acting as competitive inhibitors of downstream applications. We evaluated the LOOXSTER® Enrichment Kit to separate eukaryotic and prokaryotic DNA in submucosal intestinal tissue samples having a low microbial biomass and to determine the effects of enrichment on 16s rRNA microbiota sequencing. The enrichment kit reduced the amount of human DNA in the samples 40–70% resulting in a 3.5-fold increase in the number of 16s bacterial gene sequences detected on the Illumina MiSeq platform. This increase was accompanied by the detection of 41 additional bacterial genera and 94 tentative species. The additional bacterial taxa detected accounted for as much as 25% of the total bacterial population that significantly altered the relative prevalence and composition of the intestinal microbiota. The ability to reduce the competitive inhibition created by human DNA and the concentration of bacterial DNA may allow metagenomics to be performed on complex tissues containing a low bacterial biomass.

Treatment of Nitrate-Rich Saline Effluent by Using Citrate-Rich Waste as Carbon Source and Electron Donor in a Single-Stage Activated Sludge Reactor

Disposing of nitrate-containing effluents from seawater-fed intensive aquacultural applications is a major environmental problem. A possible solution is to mix nitrate-rich effluents from marine recirculating aquaculture systems (RASs) with citrate-rich liquid wastes (CLW), a common by-product of the food industry. Where possible, such strategy can alleviate two environmental problems simultaneously, in a cost-effective fashion. However, concerns are often raised regarding secondary pollution stemming from the use of CLW, particularly related to phosphorus and heavy metals. This work showed that both phosphorus and heavy metal were completely absorbed by the bacterial sludge generated in the process, indicating low environmental risk associated with the disposal of the treated effluent to the environment. Operation of continuous stirred-tank reactor (CSTR) single-sludge denitrification reactor with CLW as electron and carbon donor resulted in high nitrate removal efficiency (>95 %) and denitrification rate of up to 1.6 g NO3-N L−1 reactor day−1 along with low bacterial biomass yield [0.23 g chemical oxygen demand (COD) new cells g−1 COD citrate]. Moreover, the use of CLW was found to be environmentally safe and equally efficient to the use of traditional, costly carbon sources such as methanol and acetic acid, rendering this alternative attractive for treatment of nitrate-rich saline effluents.

Dynamics and functions of bacterial communities in bark, charcoal and sand filters treating greywater

This study explored the effects of greywater application on the dynamics and functions of biofilms developed in bark, activated charcoal and sand filters used for removal of organic matter and nitrogen. Duplicate columns (20 cm diameter, 60 cm deep) were packed with bark, charcoal or sand with effective size 1.4 mm and uniformity coefficient 2.2, and dosed with 32 L m−2 day−1 of an artificial greywater (14 g BOD5 m−2 day−1) for 116 days. Potential respiration rate (PRR), determined in filter samples after addition of excess glucose, and bacterial diversity and composition, analysed by 454-pyrosequencing of bacterial 16S ribosomal DNA, were measured at different times and depths in the filters. The bark and charcoal filters were more efficient in removing BOD5 than the sand (98, 97% and 75%, respectively). The highest PRR in the 0–2 cm layer of the columns on day 84 was found in the bark filters, followed by the charcoal and sand filters (632 ± 66, 222 ± 34 and 56 ± 2 mg O2 L−1, respectively; n = 2). Bacterial community in the bark filters showed the highest richness. The charcoal and sand filters both developed more diverse and dynamic (changing over time and depth) bacterial communities than the bark. In addition to the greywater, the lignocelluosic composition of the bark and its lower pH probably selected for the bacterial community structure and the organic content provided additional substrate, as shown by its higher PRR and its different nitrifying bacterial genera. In the oligotrophic charcoal and sand, the composition of the greywater itself defined the bacterial community. Thus, the initially low bacterial biomass in the latter filters was enriched over time, allowing a diversified bacterial community to develop. The top layers of the bark and charcoal filters displayed a high dominance of Rhizobium, Pseudomonas and Acinetobacter, which were less evident in the 60 cm layer, whereas in the sand filters these genera were prominent at both 0–2 cm and 60 cm. The PRR, bacterial diversity and composition profiles indicated that organic matter degradation occurred mainly in the top 20 cm of the bark and charcoal filters. This means that bark and charcoal filters could be designed to be shallower than sand filters.

Meta'omic Analytic Techniques for Studying the Intestinal Microbiome

Nucleotide sequencing has become increasingly common and affordable, and is now a vital tool for studies of the human microbiome. Comprehensive microbial community surveys such as MetaHit and the Human Microbiome Project have described the composition and molecular functional profile of the healthy (normal) intestinal microbiome. This knowledge will increase our ability to analyze host and microbial DNA (genome) and RNA (transcriptome) sequences. Bioinformatic and statistical tools then can be used to identify dysbioses that might cause disease, and potential treatments. Analyses that identify perturbations in specific molecules can leverage thousands of culture-based isolate genomes to contextualize culture-independent sequences, or may integrate sequence data with whole-community functional assays such as metaproteomic or metabolomic analyses. We review the state of available systems-level models for studies of the intestinal microbiome, along with analytic techniques and tools that can be used to determine its functional capabilities in healthy and unhealthy individuals.

Chickpea genotypes shape the soil microbiome and affect the establishment of the subsequent durum wheat crop in the semiarid North American Great Plains

Accumulating evidence supports the feasibility of creating biotic soil environments that promote root health using selected plant genotypes. Five years of field experimentation conducted in the semiarid grasslands of North America revealed genotypic variation in the influence of chickpea on the composition of the soil microbial community and on the establishment of the subsequent crop. A 2-year experiment documented the effects of four chickpea cultivars on the arable soil microbiome using cultural methods, the cloning and sequencing of soil-extracted DNA, and fatty acid methyl ester profiling. Cultivar CDC Frontier was characterized by low bacterial biomass, whereas Amit and CDC Anna selected similarly structured bacterial communities but contrasting soil fungal communities. Amit and CDC Anna became colonized by arbuscular mycorrhizal (AM) fungi to the same extent, but the arable soil planted with CDC Anna hosted the highest level of culturable fungal diversity, whereas the soil planted with Amit hosted the lowest. The highest diversity of culturable fungi and the richness of AM fungal ribotypes (11) were also associated with CDC Anna. Amit was preferentially associated with the antagonist species Penicillium canescens. Higher durum wheat stand density was found after CDC Anna than after Amit, indicating that microbial diversity is an important feature of productive soils. The influence of chickpea genotype on the arable soil microbiome and on the establishment of the subsequent durum wheat crop was related to the soil water reserve at depths of 30–120 cm and was eliminated when the chickpea crops experienced drought. Genetic variation in the influence of chickpea on the soil microbiome suggests the possibility of selecting genotypes to engineer beneficial soil biotic environments. Inadequate levels of soil water could limit the success of this strategy, however, in rainfed cropping systems of the semiarid grasslands of North America.

Microalgae: a sustainable feed source for aquaculture

The need for nutritional sources safer than traditional animal products has renewed interest generally in plants and particularly in microalgae. Microalgae have diverse uses in aquaculture, their applications are mainly to provide nutrition and to enhance the colour of the flesh of salmonids. The larvae of molluscs, echinoderms and crustaceans as well as some fish larvae feed on microalgae. Several studies have confirmed that a live multi-specific, low bacterial and microalgal biomass remains essential for shellfish hatcheries. Major advances are expected from new production system, designs and operations from batch run open tanks to more sophisticated continuously-run and closed loop reactors. Currently, studies are underway to examine the cost-effectiveness of the on- and off-site microalgal production systems which can only be achieved by substantial scaling-up and improved quality control. In order to attain sustainability in the usage of microalgae, a systems-based approach is required which integrates different fields such as biotechnology, bioprocess and management procedures.

Use of Filamentous Fungi for Wastewater Treatment and Production of High Value Fungal Byproducts: A Review

Conventional biological wastewater treatment generates large amounts of low value bacterial biomass. The treatment and disposal of this excess bacterial biomass, also known as waste activated sludge, accounts for about 40–60% of the wastewater treatment plant operation cost. A different form of biomass with a higher value could significantly change the economics of wastewater treatment. Fungi could offer this benefit over bacteria in wastewater treatment processes. The biomass produced during fungal wastewater treatment has, potentially, a much higher value than that from the bacterial activated sludge process. The fungi can be used to derive valuable biochemicals and can also be used as a protein source. Various high-value biochemicals are produced by commercial cultivation of fungi under aseptic conditions using expensive substrates. Food-processing wastewater is an attractive alternative as a source of low-cost organic matter and nutrients to produce fungi with concomitant wastewater purification. This review summarizes various findings in fungal wastewater treatment, particularly focusing on byproduct recovery during wastewater treatment. This review also provides an overview on performance of fungal treatment systems under various operational conditions. Important factors such as pH, temperature, hydraulic and solids retention time, nonaxenic and axenic operation, and others that affect the fungal treatment system are discussed. Moreover, certain important practical issues such as bacterial contamination under nonaseptic operation are also covered. The goal of the review paper is to evaluate the feasibility of cultivating fungi during wastewater treatment for deriving valuable biochemicals.

A mixture of grass and clover combines the positive effects of both plant species on selected soil biota

The introduction of N 2-fixing white clover ( Trifolium repens) in grassland is a management measure that may contribute to sustainable grassland systems by making them less dependent on inorganic fertilizers. However, little is known about the impact of this measure on soil biota and ecosystem services. We investigated earthworms, nematodes, bacteria and fungi in an experiment in which white clover-only and a mixture of grass and white clover without fertilization were compared with grass-only with and without fertilization. In comparison with grass-only, white clover-only had a lower total root biomass and a lower C/N-ratio in the above- and below-ground plant biomass. These plant characteristics resulted in a lower bacterial biomass, a lower fungal biomass, a higher proportion of bacterivorous nematode dauerlarvae, a lesser proportion of herbivorous nematodes and a greater abundance of earthworms in clover-only. The quantity and quality (C/N-ratio) of the above- and below-ground plant biomass in the mixture of grass and white clover (20–30% clover in the DM) was comparable with grass fertilized with 150 kg N ha −1 of inorganic fertilizer. Differences between these treatments might show specific clover effects in the grass–clover mixture on soil biota other than quantity and C/N-ratio of the litter. However, the only differences were a higher proportion of bacterivorous nematode dauerlarvae and a different nematode community composition in grass–clover. The soil structure in white clover-only showed a higher proportion of angular blocky elements, a lower penetration resistance, a higher number of earthworm burrows, a higher potential N-mineralization and respiration than the soil in grass-only. This suggests that clover stimulates the ecosystem services of water infiltration and supply of nutrients, but is less conducive to soil structure maintenance. The grass–clover mixture differed from grass-only in a higher respiration and from clover-only in a higher percentage of soil crumbs. We suggest that when clover is introduced in grassland to reduce the reliance on inorganic fertilizer, the mixture of grass and clover maintains the positive impact of grass roots on soil structure and increases the supply of nutrients via the soil food web. Thus, a grass–clover mixture combines the agronomic benefits of the two plant types.

Dissolved organic carbon distributions in the Bransfield and Gerlache Straits, Antarctica

Abstract During FRUELA’95 cruise, seawater samples were collected at the Bransfield and Gerlache Straits for the analysis of dissolved organic carbon (DOC) profiles throughout the water column. An excess of DOC probably derived from phytogenic material was observed in the upper mixed layer (UML; average: +22±13 μmol C l−1), compared to the constant concentration of refractory DOC below 400 m (44±4 μmol C l−1). The average excess DOC concentration was higher than the particulate organic carbon concentration indicating the major contribution of DOC to carbon export in this area. However, large spatial variability of DOC in the upper mixed layer (52–102 μmol C l−1) was observed: excess DOC contributed from 15% to 57% to the actual DOC concentration. Maximum average DOC concentrations in the UML were recorded in the Gerlache Strait (71 μmol C l−1) and in the Gerlache–Bransfield confluence (80 μmol C l−1), whereas minimum values were recorded in the Bransfield Strait (61 μmol C l−1). Several shelf and slope stations showed a slight increase of DOC (5–10 μmol C l−1) in the deep layer which might be related to organic matter release from the underlying sediments. Considering the net DOC release from phytoplankton, the low bacterial biomass and the reduced vertical DOC export, the DOC excess could build up in about 6 days for most of the sampling stations. The probable fate of the DOC excess is the eastwards horizontal transport by the Bransfield Current out of the study area.

Bacteria-flagellate interactions in the microbial food web of the oligotrophic subtropical North Pacific

The number and relative strengths of trophic linkages in the microbial community of the oligotrophic subtropical North Pacific were studied in 12 experiments from August 1998 to April 1999 at Stn ALOHA (100 km north of Oahu, Hawaii). Collected seawater was manipulated by sequential size-fractionation to truncate the food web at different organism sizes (1, 2, 5, 10 and 20 µm), and the response variable, net bacterial growth rate, was assessed from flow cytometric analyses of the changes in cell abundance (combined heterotrophic bacteria and Prochlorococcus) after 24 h incuba- tions. The corresponding size structure of the protistan grazer assemblage was measured microscop- ically. With a coefficient of variability of 7% and a 2-fold range overall, total bacterial abundance dis- played relatively low temporal variability. Despite the relative constancy of standing stock, however, microbial community interactions varied markedly among the experiments. For experiments con- ducted at higher levels of bacterial biomass, the bacteria showed little growth response to the removal of predators and may have been resource limited. In contrast, the growth response was high- est when conditions were defined by relatively low bacterial biomass and high heterotrophic flagel- late biomass. Trophic cascades were evident only at intermediate to high levels of bacterial biomass, and may appear in transitions between high and low levels of bacterial biomass. These results sug- gest that resources and predators oscillate in importance in regulating open-ocean microbial popula- tions. In such oscillations, the indirect influences of a protistan predatory chain may determine the balance between resource limitation and strong predatory control.