Food processing can generate large amounts of carbohydrate-rich waste that inevitably has environmental and social impacts. Meanwhile, certain heterotrophic marine microorganisms, including algae and thraustochytrids, have the potential to convert carbohydrate-rich substrates into oil-rich biomass over relatively short time frames. To assess the merits of this apparent synergy, an initial conceptual process was developed based on the use of raw potato processing waste as feed in an algal bioreactor to produce bio-oil for further use within the food industry. A practical flowsheet was established with a conventional 200 kL bioreactor whereby the unit processes were identified, the mass balance developed, and estimates made of the various material and energy demands. These inputs were used to develop a baseline life cycle assessment (LCA) model and to identify opportunities for reducing environmental impacts. With the functional unit (FU) being 1 tonne cooking oil, the baseline configuration had a greenhouse gas (GHG) footprint of 2.4 t CO2-e/FU, which is comparable to conventional process routes. More detailed LCA revealed that electricity for stirring the bioreactor contributed approximately 78% of the total GHG footprint. By adjusting the operating conditions, the most promising scenario produced 0.85 t CO2-e/FU—approximately four times less than the conventional process—and shows the potential advantages of applying LCA as a tool to develop and design a new production process.

Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria , Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30 ° of latitude and ~38 ° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.

With intensification of interest in microalgae as a source of biomass for biofuel production, rapid methods are needed for lipid screening of cultures. In this study, near-infrared reflectance spectroscopy (NIRS) was assessed as a method for analysing lipid (specifically, total fatty acid methyl esters (FAME) obtainable from processing) and biomass in late logarithmic and stationary phase cultures of the green alga Kirchneriella sp. and the eustigmatophyte Nannochloropsis sp. Culture samples were filtered, scanned by NIRS and chemically analysed; by combining these sets of information, models were developed to predict total biomass, FAME content and FAME as a percentage of dry weight in samples. Chemically derived (actual) and NIRS-predicted data were compared using the coefficient of determination (R 2) and the ratio of the standard deviation (SD) of actual data to the SD of NIRS prediction (RPD). For Kirchneriella sp. samples, models gave excellent prediction (R 2 ≥ 0.96; RPD ≥ 4.8) for all parameters. For Nannochloropsis sp., the model metrics were less favourable (R 2 = 0.84–0.94; RPD = 2.5–4.2), though sufficient to provide estimations that could be useful for screening purposes. This technique may require further validation and comparison with other species, but this study shows the potential of the NIRS as a rapid screening method (e.g. up to 200 sample analyses per day) for estimating FAME or other microalgal constituents and encourages further investigation.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Treatment of wastewater while producing microalgal biomass is receiving ever-increasing attention, particularly in the biofuels arena. In this study, a wastewater chlorophyte isolate, Kirchneriella sp., was tested for its ability to be mass cultivated, utilize nutrients from defined media and wastewater, and produce bioproducts of commercial interest. Growth studies were carried out in various systems at scales up to 60 L, with Kirchneriella sp. showing an excellent amenability to being cultured. Biomass concentrations of greater than 1 g L-1 were consistently achieved, nitrogen and phosphorus uptake was rapid, and stable medium-term cultures were maintained. Nitrogen limitation affected biomass yield, fatty acid methyl ester (FAME) yield, and cetane index. In contrast, a low phosphorus condition had no effect. Kirchneriella sp. showed an ability to produce several products of commercial value, including carbohydrate-rich biomass, FAME/biodiesel and the pigments beta,beta-carotene and lutein. Crown Copyright (C) 2012 Published by Elsevier Ltd. All rights reserved.

The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA) gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively), combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

The transgenic aerobic synthesis of long-chain polyunsaturated fatty acids (LC-PUFA) will in most land plants commence with either a Delta 6-desaturation or a Delta 9-elongation. Numerous Delta 6-desaturases have been characterized, but only one Delta 9-elongase has been reported in peer-reviewed literature. In the present study, we describe the isolation of three additional Delta 9-elongases from the class Haptophyceae and demonstrate that the Delta 9-elongase group contains highly conserved regions, which differentiate them from other ELO-type elongases. One such important difference is the presence of an LQxFHH motif instead of the usual LHxYHH motif, a feature that should simplify further gene discovery efforts in this group of enzymes. Moreover, the identification of the Pavlova salina (N. Carter) J. C. Green Delta 9-elongase completes the isolation of the entire P. salina docosahexaenoic acid (DHA) pathway, and we describe the assembly of this pathway in Nicotiana benthamiana. Finally, we comment on possible explanations for the widespread presence of the Delta 6-desaturated fatty acid stearidonic acid (SDA, 18:4 Delta 6,9,12,15) in the plastidial lipids of organisms using the Delta 9-elongase pathway.

The production of long-chain polyunsaturated fatty acids from precursor molecules linoleic acid (LA; 18:2ω6) and α-linolenic acid (ALA; 18:3ω3) is catalysed by sequential desaturase and elongase reactions. We report the isolation of a front-end Δ6-desaturase gene from the microalgae Ostreococcus lucimarinus and two elongase genes, a Δ6-elongase and a Δ5-elongase, from the microalga Pyramimonas cordata. These enzymes efficiently convert their respective substrates when transformed in yeast (39–75% conversion for ω3 substrate fatty acids), and the Δ5-elongase in particular displays higher elongation efficiency (75% for conversion of eicosapentaenoic acid (20:5ω3) to docosapentaenoic acid (22:5ω3)) than previously reported genes. In addition, the Δ6-desaturase is homologous with acyl-CoA desaturases and shows a strong preference for the ω3 substrate ALA.

The marine microalga Pavlova salina produces lipids containing approximately 50% omega-3 long chain polyunsaturated fatty acids (LC-PUFA) such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). Three cDNA sequences, designated PsD4Des, PsD5Des, PsD8Des, were isolated from P. salina and shown to encode three front-end desaturases with Delta4, Delta5 and Delta8 specificity, respectively. Southern analysis indicated that the P. salina genome contained single copies of all three front-end fatty acid desaturase genes. When grown at three different temperatures, analysis of fatty acid profiles indicated P. salina desaturation conversions occurred with greater than 95% efficiency. Real-Time PCR revealed that expression of PsD8Des was higher than for the other two genes under normal growth conditions, while PsD5Des had the lowest expression level. The deduced amino acid sequences from all three genes contained three conserved histidine boxes and a cytochrome b(5) domain. Sequence alignment showed that the three genes were homologous to corresponding desaturases from other microalgae and fungi. The predicted activities of these three front-end desaturases leading to the synthesis of LC-PUFA were also confirmed in yeast and in higher plants.

A novel technique was developed for the flocculation of marine microalgae commonly used in aquaculture. The process entailed an adjustment of pH of culture to between 10 and 10.6 using NaOH, followed by addition of a non-ionic polymer Magnafloc LT-25 to a final concentration of 0.5 mg L-1. The ensuing flocculate was harvested, and neutralised giving a final concentration factor of between 200- and 800-fold. This process was successfully applied to harvest cells of Chaetoceros calcitrans, C. muelleri, Thalassiosira pseudonana, Attheya septentrionalis, Nitzschia closterium, Skeletonema sp., Tetraselmis suecica and Rhodomonas salina, with efficiencies >= 80%. The process was rapid, simple and inexpensive, and relatively cost neutral with increasing volume (cf. concentration by centrifugation). Harvested material was readily disaggregated to single cell suspensions by dilution in seawater and mild agitation. Microscopic examination of the cells showed them to be indistinguishable from corresponding nonflocculated cells. Chlorophyll analysis of concentrates prepared from cultures of <= 130 L showed minimal degradation after 2 weeks storage. Concentrates of T pseudonana prepared using pH-induced flocculation gave better growth of juvenile Pacific oysters (Crassostrea gigas) than concentrates prepared by ferric flocculation, or centrifuged concentrates using a cream separator or laboratory centrifuge. In follow up experiments, concentrates prepared from 1000 L Chaetoceros muelleri cultures were effective as supplementary diets to improve the growth of juvenile C. gigas and the scallop Pecten fumatus reared under commercial conditions, though not as effective as the corresponding live algae. The experiments demonstrated a proof-of-concept for a commercial application of concentrates prepared by flocculation, especially for use at a remote nursery without on-site mass-algal culture facilities. (c) 2006 Elsevier B.V. All rights reserved.

Nine microalgal species from the classes Bacillariophyceae, Cryptophyceae, Prymnesiophyceae and Dinophyceae were isolated from Australian waters, cultured to stationary phase and analyzed for their lipid and fatty acid composition and yield. Five species ( Pavlova pinguis , Heterocapsa niei , Proteomonas sulcata , Navicula jeffreyi and Thalassiosira pseudonana ) produced high proportions of triacylglycerol (TAG: 22–57% total lipid). An unidentified Navicula -like diatom (CS-786), despite having a low TAG content, had the highest EPA yield (5.8 mg L −1 ), due to high biomass and a high relative proportion of EPA. Heterocapsa niei had the highest DHA yield (2.9 mg L −1 ), due to a high cellular lipid and DHA content (171 pg cell −1 and 13.7 pg cell −1 , respectively) despite its relatively low biomass. The desirable PUFA composition and yield of both diatom CS-786 and H. niei make them potential candidates for optimization of biomass and PUFA production for use as live-feeds in aquaculture. In addition, H. niei may have potential as a source of DHA for other uses. Low proportions (< 1.2%) of 24:6( n −3) accompanied by trace proportions of 24:5( n −6) were detected in most strains, while 28:8( n −3) was found in dinoflagellates and also in the prymnesiophyte P. pinguis . All non-diatomaceous species contained 26:7( n −3) in minor quantities. This is the first time these unusual C 24 and C 26 PUFA have been reported in microalgae and the first report of C 28 PUFA in a microalga other than dinoflagellates. Possible biosynthetic reasons why these might occur in stationary phase cultures are considered and the likely dietary transfer of these PUFA to higher aquatic life is discussed.