Ecology of uncultivated oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches

The ecology of the uncultured, but large and morphologically conspicuous, rumen bacterium Oscillospira spp. was studied. Oscillospira-specific 16S rRNA gene sequences were detected in North American domestic cattle, sheep from Australia and Japan, and Norwegian reindeer. Phylogenetic analysis of the sequences obtained allowed definition of three operational taxonomic units within the Oscillospira clade. Consistent with this genetic diversity, we observed atypical smaller morphotypes by using an Oscillospira-specific fluorescence in situ hybridization probe. Despite the visual disappearance of typical large Oscillospira morphotypes, the presence of Oscillospira spp. was still detected by Oscillospira-specific PCR in the rumen of cattle and sheep. These observations suggest the broad presence of Oscillospira species in various rumen ecosystems with the level, and most likely the morphological form, dependent on diet. An ecological analysis based on enumeration of the morphologically conspicuous, large-septate form confirms that the highest counts are associated with the feeding of fresh forage diets to cattle and sheep and in two different subspecies of reindeer investigated.

Bacterial Community Structure in the Hindgut of Wild and Captive Dugongs (Dugong dugon)

Dugongs (Dugong dugon) are marine mammals that obtain nutrients through hindgut fermentation of seagrass, however, the microbes responsible have not been identified. This study used denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing to profile hindgut bacterial communities in wild dugongs. Faecal samples obtained from 32 wild dugongs representing four size/maturity classes, and two captive dugongs fed on cos lettuce were screened using DGGE. Partial 16S rRNA gene profiles of hindgut bacteria from wild dugong calves and juveniles were grouped together and were different to those in subadults and adults. Marked differences between hindgut bacterial communities of wild and captive dugongs were also observed, except for a single captive whose profile resembled wild adults following an unsuccessful reintroduction to the wild. Pyrosequencing of hindgut communities in two wild dugongs confirmed the stability of bacterial populations, and Firmicutes (average 75.6% of Operational Taxonomic Units [OTUs]) and Bacteroidetes (19.9% of OTUs) dominated. Dominant genera were Roseburia, Clostridium, and Bacteroides. Hindgut microbial composition and diversity in wild dugongs is affected by ontogeny and probably diet. In captive dugongs, the absence of the dominant bacterial DNA bands identified in wild dugongs is probably dependent upon prevailing diet and other captive conditions such as the use of antibiotics. This study represents a first step in the characterisation of a novel microbial ecosystem-the marine hindgut of Sirenia.

A simple, one-tube assay for the simultaneous detection and diagnosis of ten Australian poultry Eimeria

Coccidiosis is a costly worldwide enteric disease of chickens caused by parasites of the genus Eimeria. At present, there are seven described species that occur globally and a further three undescribed, operational taxonomic units (OTUs X, Y, and Z) that are known to infect chickens from Australia. Species of Eimeria have both overlapping morphology and pathology and frequently occur as mixed-species infections. This makes definitive diagnosis with currently available tests difficult and, to date, there is no test for the detection of the three OTUs. This paper describes the development of a PCR-based assay that is capable of detecting all ten species of Eimeria, including OTUs X, Y, and Z in field samples. The assay is based on a single set of generic primers that amplifies a single diagnostic fragment from the mitochondrial genome of each species. This one-tube assay is simple, low-cost, and has the capacity to be high throughput. It will therefore be of great benefit to the poultry industry for Eimeria detection and control, and the confirmation of identity and purity of vaccine strains.

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas

Divergent genetic selection for wool growth as a single trait has led to major changes in sheep physiology and metabolism, including variations in rumen microbial protein production and uptake of α-amino nitrogen in portal blood. This study was conducted to determine if sheep with different genetic merit for wool growth exhibit distinct rumen bacterial diversity. Eighteen Merino wethers were separated into groups of contrasting genetic merit for clean fleece weight (CFW; low: WG− and high: WG+) and fed a blend of oaten and lucerne chaff diet at two levels of intake (LOI; 1 or 1.5 times maintenance energy requirements) for two seven-week periods in a crossover design. Bacterial diversity in rumen fluid collected by esophageal intubation was characterized using 454 amplicon pyrosequencing of the V3/V4 regions of the 16S rRNA gene. Bacterial diversity estimated by Phylogenetic distance, Chao1 and observed species did not differ significantly with CFW or LOI; however, the Shannon diversity index differed (P=0.04) between WG+ (7.67) and WG− sheep (8.02). WG+ animals had a higher (P=0.03) proportion of Bacteroidetes (71.9% vs 66.5%) and a lower (P=0.04) proportion of Firmicutes (26.6% vs 31.6%) than WG− animals. Twenty-four specific operational taxonomic units (OTUs), belonging to the Firmicutes and Bacteroidetes phyla, were shared among all the samples, whereas specific OTUs varied significantly in presence/abundance (P<0.05) between wool genotypes and 50 varied (P<0.05) with LOI. It appears that genetic selection for fleece weight is associated with differences in rumen bacterial diversity that persist across different feeding levels. Moderate correlations between seven continuous traits, such as methane production or microbial protein production, and the presence and abundance of 17 OTUs were found, indicating scope for targeted modification of the microbiome to improve the energetic efficiency of rumen microbial synthesis and reduce the greenhouse gas footprint of ruminants.

A molecular survey of Eimeria in chickens across Australia

Coccidiosis is a costly enteric disease of chickens caused by protozoan parasites of the genus Eimeria. Disease diagnosis and management is complicated since there are multiple Eimeria species infecting chickens and mixed species infections are common. Current control measures are only partially effective and this, combined with concerns over vaccine efficacy and increasing drug resistance, demonstrates a need for improved coccidiosis diagnosis and control. Before improvements can be made, it is important to understand the species commonly infecting poultry flocks in both backyard and commercial enterprises. The aim of this project was to conduct a survey and assessment of poultry Eimeria across Australia using genetic markers, and create a collection of isolates for each Eimeria species. A total of 260 samples (faecal or caecal) was obtained, and survey results showed that Eimeria taxa were present in 98% of commercial and 81% of backyard flocks. The distribution of each Eimeria species was widespread across Australia, with representatives of all species being found in every state and territory, and the Eimeria species predominating in commercial flocks differed from those in backyard flocks. Three operational taxonomic units also occurred frequently in commercial flocks highlighting the need to understand the impact of these uncharacterised species on poultry production. As Eimeria infections were also frequent in backyard flocks, there is a potential for backyard flocks to act as reservoirs for disease, especially as the industry moves towards free range production systems. This Eimeria collection will be an important genetic resource which is the crucial first step in the development of more sophisticated diagnostic tools and the development of new live vaccines which ultimately will provide savings to the industry in terms of more efficient coccidiosis management.

Microbial communities in Pb contaminated boreal forest soil

Lead contamination in the environment is of particular concern, as it is a known toxin. Until recently, however, much less attention has been given to the local contamination caused by activities at shooting ranges compared to large-scale industrial contamination. In Finland, more than 500 tons of Pb is produced each year for shotgun ammunition. The contaminant threatens various organisms, ground water and the health of human populations. However, the forest at shooting ranges usually shows no visible sign of stress compared to nearby clean environments. The aboveground biota normally reflects the belowground ecosystem. Thus, the soil microbial communities appear to bear strong resistance to contamination, despite the influence of lead. The studies forming this thesis investigated a shooting range site at Hälvälä in Southern Finland, which is heavily contaminated by lead pellets. Previously it was experimentally shown that the growth of grasses and degradation of litter are retarded. Measurements of acute toxicity of the contaminated soil or soil extracts gave conflicting results, as enchytraeid worms used as toxicity reporters were strongly affected, while reporter bacteria showed no or very minor decreases in viability. Measurements using sensitive inducible luminescent reporter bacteria suggested that the bioavailability of lead in the soil is indeed low, and this notion was supported by the very low water extractability of the lead. Nevertheless, the frequency of lead-resistant cultivable bacteria was elevated based on the isolation of cultivable strains. The bacterial and fungal diversity in heavily lead contaminated shooting sectors were compared with those of pristine sections of the shooting range area. The bacterial 16S rRNA gene and fungal ITS rRNA gene were amplified, cloned and sequenced using total DNA extracted from the soil humus layer as the template. Altogether, 917 sequenced bacterial clones and 649 sequenced fungal clones revealed a high soil microbial diversity. No effect of lead contamination was found on bacterial richness or diversity, while fungal richness and diversity significantly differed between lead contaminated and clean control areas. However, even in the case of fungi, genera that were deemed sensitive were not totally absent from the contaminated area: only their relative frequency was significantly reduced. Some operational taxonomic units (OTUs) assigned to Basidiomycota were clearly affected, and were much rarer in the lead contaminated areas. The studies of this thesis surveyed EcM sporocarps, analyzed morphotyped EcM root tips by direct sequencing, and 454-pyrosequenced fungal communities in in-growth bags. A total of 32 EcM fungi that formed conspicuous sporocarps, 27 EcM fungal OTUs from 294 root tips, and 116 EcM fungal OTUs from a total of 8 194 ITS2 454 sequences were recorded. The ordination analyses by non-parametric multidimensional scaling (NMS) indicated that Pb enrichment induced a shift in the EcM community composition. This was visible as indicative trends in the sporocarp and root tip datasets, but explicitly clear in the communities observed in the in-growth bags. The compositional shift in the EcM community was mainly attributable to an increase in the frequencies of OTUs assigned to the genus Thelephora, and to a decrease in the OTUs assigned to Pseudotomentella, Suillus and Tylospora in Pb-contaminated areas when compared to the control. The enrichment of Thelephora in contaminated areas was also observed when examining the total fungal communities in soil using DNA cloning and sequencing technology. While the compositional shifts are clear, their functional consequences for the dominant trees or soil ecosystem remain undetermined. The results indicate that at the Hälvälä shooting range, lead influences the fungal communities but not the bacterial communities. The forest ecosystem shows apparent functional redundancy, since no significant effects were seen on forest trees. Recently, by means of 454 pyrosequencing , the amount of sequences in a single analysis run can be up to one million. It has been applied in microbial ecology studies to characterize microbial communities. The handling of sequence data with traditional programs is becoming difficult and exceedingly time consuming, and novel tools are needed to handle the vast amounts of data being generated. The field of microbial ecology has recently benefited from the availability of a number of tools for describing and comparing microbial communities using robust statistical methods. However, although these programs provide methods for rapid calculation, it has become necessary to make them more amenable to larger datasets and numbers of samples from pyrosequencing. As part of this thesis, a new program was developed, MuSSA (Multi-Sample Sequence Analyser), to handle sequence data from novel high-throughput sequencing approaches in microbial community analyses. The greatest advantage of the program is that large volumes of sequence data can be manipulated, and general OTU series with a frequency value can be calculated among a large number of samples.

The Foraging Ecology of the Mountain Long-Eared Bat Plecotus macrobullaris Revealed with DNA Mini-Barcodes

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Bacterial diversity in activated sludge from a consecutively aerated submerged membrane bioreactor treating domestic wastewater

The bacterial diversity of activated sludge from submerged membrane bioreactor (SMBR) was investigated. A 16S rDNA clone library was generated, and 150 clones were screened using restriction fragment length polymorphism (RFLP). Of the screened clones, almost full-length 16S rDNA sequences of 64 clones were sequenced. Phylogenetic tree was constructed with a database containing clone sequences from this study and bacterial rDNA sequences from NCB1 for identification purposes. The 90.6% of the clones were affiliated with the two phyla Bacteroidetes (50%) and Proteobacteria (40%), and beta-, -gamma-, and delta-Proteobacteria accounted for 7.8%, 28.1%, and 4.7%, respectively. Minor portions were affiliated with the Actinobacteria and Firmicutes (both 3.1%). Only 6 out of 64 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species, which indicated that a substantial fraction of the clone sequences were derived from unknown taxa. Rarefaction analysis of operational taxonomic units (orrUs) clusters demonstrated that 150 clones screened were still insufficient to describe the whole bacterial diversity. Measurement of water quality parameter demonstrated that performance of the SMBR maintained high level, and the SMBR system remained stable during this study.

Plankton community composition in the Three Gorges Reservoir Region revealed by PCR-DGGE and its relationships with environmental factors

To explore the relationships between community composition and the environment in a reservoir ecosystem, plankton communities from the Three Gorges Reservoir Region were studied by PCR-denaturing gradient gel electrophoresis fingerprinting. Bacterial and eukaryotic operational taxonomic units (OTUs), generated by DGGE analysis of the PCR-amplified 16S and 18S rRNA genes, were used as surrogates for the dominant "biodiversity units". OTU composition among the sites was heterogeneous; 46.7% of the total bacteria] OTUs (45) and 64.1% of the eukaryotic OTUs (39) were identified in less than half of the sampling sites. Unweighted pair group method with arithmetic averages (UPGMA) clustering of the OTUs suggested that the plankton communities in the Xiangxi Rive sites were not always significantly different from those from the Yangtze River sites, despite clear differences in their environmental characterizations. Canonical correspondence analysis (CCA) was applied to further investigate the relationships between OTU composition and the environmental factors. The first two CCA ordination axes suggested that the bacterial community composition was primarily correlated with the variables of NO3--N, dissolved oxygen (DO), and SiO32--Si, whereas, the eukaryotic community was mainly correlated with the concentrations of DO, PO43--P, and SiO32--Si.

沙蜥属部分物种分类性状评价

沙蜥属Phrynocephalus Kaup，1825隶属于爬行纲（Reptilia）有鳞目（Squamata）蜥蜴亚目（Lacertilia）鬣蜥科（Agamidae），是欧亚大陆荒漠和稀疏草原常见蜥蜴。沙蜥属的分类及系统演化关系、地理分布格局与新生代第三纪以来古地中海的变迁、青藏高原的抬升及亚洲内陆干旱荒漠化的过程有密切的关系，长期以来有关沙蜥属的研究一直受到中外学者们的关注。由于沙蜥属地理分布广、形态变异大、体色和斑纹变化复杂，虽然前人使用过许多形态性状来描述和分类沙蜥属物种，但是仍然存在许多问题。性状的分类学意义不明确是造成这些问题的主要原因之一，因此本研究针对沙蜥属常用的鉴别性状进行分类意义的分析，希望能对沙蜥属物种鉴定及分类学其它研究有所裨益。 中国沙蜥属物种主要分布于西北的干旱荒漠区域及青藏高原的大部分地区，大约为18种。 本文研究了中国境内12种沙蜥：青海沙蜥（Phrynocephalus vlangalii）、西藏沙蜥（P. theobaldi）、南疆沙蜥（P. forsythii）、变色沙蜥（P. versicolor）、旱地沙蜥（P. helioscopus）、荒漠沙蜥（P. przewalskii）、乌拉尔沙蜥（P. guttatus）、草原沙蜥（P. frontalis）、叶城沙蜥（P. axillaris）、白稍沙蜥（P. koslowi）、无斑沙蜥（P. immaculatus）和白条沙蜥（P. albolineatus），对它们的65项外部形态性状进行了观察和测量，其中数量性状29项、质量性状36项。评价了这些性状的序级性、间断性和代表性，结论如下： 1. 对于数量性状，得出了适合各级分类的数值区间； 2. 给出了在不同序级上适合分类的质量性状。 并利用各性状评价的结果，给出12种沙蜥的检索表，以及对中国沙蜥物种某些尚存在争议的问题进行了探讨。 详细记录了青海沙蜥红原亚种的骨骼系统，首次发现并命名了肘骨（elbow bone）和垫骨（stepping bone），为沙蜥属系统学研究补充了骨骼方面的证据；解剖了乌拉尔沙蜥、旱地沙蜥、荒漠沙蜥的雌体和雄体的骨骼系统，并在14项骨骼形态性状上对这3种沙蜥进行了比较。 Phrynocephalus （Squamata，Agamidae） is a familiar genus of lizards inhabited desert and sparse steppes in Eurasia. The taxonomics, phylogenetics and distribution pattern of Phrynocephalus are relative intensely to these events: the vicissitudes of the archaic Mediterranean sea since the Cainozoic, the uplift of Qingzang Plateau and the expending arid areas in the inland of Asia. Owing to the wide distribution, the large variability of the morphology and the different colors in Phrynocephalus, it is difficult to identify them. Tough many morphological characters are used to describe and discriminate them，a lot of questions still exist. One of the most important reasons is the confusion in the morphological characters. In this study, we demonstrate the validity and the invalidity of the familiar characters. There are about 18 species of the genus Phrynocephalus in China, which exist in arid desert in Northwest China and Qingzang Plateau. Twelve Chinese species was analyzed in this paper. They are P. vlangalii，P. theobaldi，P. forsythia，P. versicolor，P. helioscopus，P. przewalskii，P. guttatus，P. frontalis，P. axillaris，P. koslowi，P. immaculatus，P. albolineatus. We measure 29 quantitative characters and observe 36 qualitative characters in each individual. Through analyzing these characters, we made some conclusions as follows: 1. to every quantitative character, we get a clear numeric area to discriminate the different operational taxonomic units. 2. we chose the valid qualitative characters in these operational taxonomic units. This paper is the first to describe the “elbow bone”, which is a bone in pectoral appendage equivalent to patella，and “stepping bone”, which is a bone under carpal. A detailed description of the skeletal system of female Phrynocephalus vlangalii hongyuanensis was conducted. We also anatomise the skeletal systems of three species: P. guttatus，P. przewalskii，P. helioscopus, and compare or contrast 14 skeletal characters in them. What’s more，this paper offers some suggestions to the questions of Chinese Phrynocephalus species and keys to 12 species of Phrynocephalus basing on our conclusions on the evaluation of the morphological characters.

鄂霍次克海天然气水合物区与东海内陆架泥质区沉积物古菌多样性研究

为研究鄂霍次克海天然气水合物区沉积物古菌、甲烷厌氧氧化古菌和硫酸盐还原细菌的多样性分布，我们以PCR技术为基础构建mcrA、dsrAB和古菌16S rRNA 基因文库。对所获得的序列进行系统进化和统计学分析发现：鄂霍次克海古菌类群主要为Marine Benthic Group D (MBG-D)、Marine Benthic Group B (MBG-B)、Marine Crenarchaeotic Group I(MG- I)，另外少量古菌16S rRNA基因序列为Anaerobic Methanotrophs 2c（ANME-2c），主要分布在LV39-25H岩心的表层沉积物中。LV39-40H岩心表层的古菌群落结构与其他六个层位古菌群落结构相比有着显著的差异。mcrA基因序列主要为催化甲烷厌氧氧化的古菌ANME-2（c和d簇），在所研究的各个层位的沉积物中均广泛分布。少量的ANME-1（a簇）发现于LV39-40H岩心表层以下的沉积物中。产甲烷古菌数目不多，集中分布在LV39-25H岩心200cm和LV39-40H岩心180cm的沉积物中。dsrAB基因文库分析表明硫酸盐还原细菌种类丰富，表层沉积物中硫酸盐还原细菌多样性最高。在两个岩心所有层位的沉积物中都有一定数量的克隆属于DSS簇，它们可能与ANME共生催化甲烷的厌氧氧化作用。总之，所有数据表明在鄂霍次克海天然气水合物区存在着较活跃的甲烷厌氧氧化作用，揭示了参与甲烷厌氧氧化作用的微生物群落结构和多样性。 为研究东海内陆架闽浙沿岸泥质区不同深度沉积物中古菌群落垂向分布特征，通过古菌16S rRNA 基因文库共得到473个有效克隆50个OTUs (Operational Taxonomic Units)。16S rRNA基因序列系统进化和统计分析发现古菌分别归属于泉古生菌（Crenarchaeota）和广古生菌（Euryarchaeota），其中以Miscellaneous Crenarchaeotic Group（MCG）为主，仅含少量的MBG-B、South African Gold Mine Euryarchaeotic Group(SAGMEG)、 ANME-3、MG- I和MBG-D。该泥质区沉积物可能存在由ANME-3催化的甲烷厌氧氧化作用，同源序列分析表明其古菌群落分布与周边环境有较大联系。UniFrac与沉积物环境因子分析表明该泥质区古菌群落垂向分布与沉积物有机质含量和粒度变化密切相关。 通过对比发现，鄂霍次克海天然气水合物区甲烷厌氧氧化古菌主要为ANME-2和少量的ANME-1，而东海内陆架泥质区甲烷厌氧氧化古菌仅为极少量的ANME-3；鄂霍次克海天然气水合物区广古生菌和泉古生菌数量各占一半，主要为MBG-D、MBG-B、MG-I。东海内陆架泥质区沉积物古菌序列主要为泉古生菌（MCG）。海域类型的不同以及有机碳含量等环境因子的差异可能是这两个海域古菌群落结构差异的主要原因.

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment

Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 atm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO2 on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.

Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.