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Abundant Taxa (abundant + taxa)
Selected AbstractsEffect of PCR amplicon size on assessments of clone library microbial diversity and community structureENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Julie A. Huber Summary PCR-based surveys of microbial communities commonly use regions of the small-subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using operational taxonomic unit (OTU)- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of c. 100, 400 and 1000 base pairs (bp) from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias and mispriming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities. [source] Key role of selective viral-induced mortality in determining marine bacterial community compositionENVIRONMENTAL MICROBIOLOGY, Issue 2 2007T. Bouvier Summary Viral infection is thought to play an important role in shaping bacterial community composition and diversity in aquatic ecosystems, but the strength of this interaction and the mechanisms underlying this regulation are still not well understood. The consensus is that viruses may impact the dominant bacterial strains, but there is little information as to how viruses may affect the less abundant taxa, which often comprise the bulk of the total bacterial diversity. The potential effect of viruses on the phylogenetic composition of marine bacterioplankton was assessed by incubating marine bacteria collected along a North Pacific coastal-open ocean transect in seawater that was greatly depleted of ambient viruses. The ambient communities were dominated by typical marine groups, including alphaproteobacteria and the Bacteroidetes. Incubation of these communities in virus-depleted ambient water yielded an unexpected and dramatic increase in the relative abundance of bacterial groups that are generally undetectable in the in situ assemblages, such as betaproteobacteria and Actinobacteria. Our results suggest that host susceptibility is not necessarily only proportional to its density but to other characteristics of the host, that rare marine bacterial groups may be more susceptible to viral-induced mortality, and that these rare groups may actually be the winners of competition for resources. These observations are not inconsistent with the ,phage kills the winner' hypothesis but represent an extreme and yet undocumented case of this paradigm, where the potential winners apparently never actually develop beyond a very low abundance threshold in situ. We further suggest that this mode of regulation may influence not just the distribution of single strains but of entire phylogenetic groups. [source] Spatial distribution and feeding habits of Pacific cod (Gadus macrocephalus) larvae in Mutsu Bay, JapanFISHERIES OCEANOGRAPHY, Issue 2 2002Tetsuya Takatsu The spatial distributions and feeding habits of Pacific cod (Gadus macrocephalus) larvae, and the spatial distributions of copepod nauplii and copepodites, their main prey, were examined in Mutsu Bay from February to March during 1989,92. Yolk-sac larvae were caught at 30,45 m depth at the bay mouth. Larvae without yolk were collected at 8,45 m depth at the bay mouth and the inner part of the bay, and large larvae were chiefly found in the bay. This geographical pattern in larval size may have been because of transport to the inner part of Mutsu Bay by the Tsugaru Warm Current. The dominant taxa of copepod nauplii and copepodites in the diet and the environment changed each year. Larvae fed mainly on abundant taxa in the environment, suggesting that larvae are opportunistic feeders. Nauplii and copepodites were abundant in the bay, especially in 1992. Copepodites were slightly more abundant in the diet of cod larvae in 1992 than in 1991, but this difference was smaller than in the environment. In addition, larvae with empty digestive tracts were scarce in 1991 and 1992. Prey concentrations in the bay in 1991 and 1992 seem to have been high enough to sustain most Pacific cod larvae. [source] Effects of floods versus low flows on invertebrates in a New Zealand gravel-bed riverFRESHWATER BIOLOGY, Issue 12 2006ALASTAIR M. SUREN Summary 1. Floods and low flows are hydrological events that influence river ecosystems, but few studies have compared their relative importance in structuring invertebrate communities. Invertebrates were sampled in riffles and runs at eight sites along 40 km of a New Zealand gravel-bed river every 1,3 months over 2.5 years, during which time a number of large flood and low flow events occurred. Flows were high in winter and spring, and low in summer and autumn. Four flow-related variables were calculated from hydrological data: flow on the day of sampling (Qsample), maximum and minimum flow between successive samples (Qmax and Qmin, respectively), and the number of days since the last bed-moving flood (Ndays). 2. The invertebrate community was summarised by relative densities of the 19 most abundant taxa and four biotic metrics [total abundance, taxon richness, the number of Ephemeroptera, Plecoptera and Trichoptera taxa (i.e. EPT richness), and per cent EPT]. Invertebrate density fluctuated greatly, and was high in summer and autumn, and low during winter and spring. Stepwise multiple regression (SMR) analysis was used to investigate relationships between the invertebrate community and season, flow, habitat and water temperature. 3. Seasonal variables were included in almost 50% of the SMR models, while flow-related variables were included in >75% of models. Densities of many taxa were negatively correlated to Qmin and Qmax, and positively correlated to Ndays, suggesting that while high flows reduced invertebrate densities, densities recovered with increasing time following a flood. Although season and flow were confounded in this study, many of the taxa analysed display little seasonal variation in abundance, suggesting that flow-related variables were more important in structuring communities than seasonal changes in density associated with life-cycles. 4. Five discrete flood and low flow events were identified and changes to invertebrate communities before and after these events examined. Invertebrate densities decreased more commonly after floods than after low flows, and there was a significant positive relationship between the number of taxa showing reductions in density and flood magnitude. Densities of most invertebrates either remained unchanged, or increased after low flow events, except for four taxa whose densities declined after a very long period (up to 9 months) of low flow. This decline was attributed to autogenic sloughing of thick periphyton communities and subsequent loss of habitat for these taxa. 5. Invertebrate communities changed more after floods and the degree of change was proportional to flood magnitude. Community similarity increased with increasing time since the last disturbance, suggesting that the longer stable flows lasted, the less the community changed. These results suggest that invertebrate communities in the Waipara River were controlled by both floods and low flows, but that the relative effects of floods were greater than even extended periods of extreme low flow. 6. Hydraulic conditions in riffles and runs were measured throughout the study. Riffles had consistently faster velocities, but were shallower and narrower than runs at all measured flows. Invertebrate density in riffles was expressed as a percentage of total density and regressed against the flow-related variables to see whether invertebrate locations changed according to flow. Significant negative relationships were observed between the per cent density of common taxa in riffles and Qsample, Qmax and Qmin. This result suggests either that these animals actively drifted into areas of faster velocity during low flows, or that their densities within riffles increased as the width of these habitats declined. [source] Do larval fishes exhibit diel drift patterns in a large, turbid river?JOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2010K. S. Reeves Summary Previous research suggested larval fishes do not exhibit a diel drift cycle in turbid rivers (transparency <30 cm). We evaluated this hypothesis in the turbid, lower Missouri River, Missouri. We also reviewed diel patterns of larval drift over a range of transparencies in rivers worldwide. Larval fishes were collected from the Missouri River primary channel every 4 h per 24-h period during spring-summer 2002. Water transparency was measured during this period and summarized for previous years. Diel drift patterns were analyzed at the assemblage level and lower taxonomic levels for abundant groups. Day and night larval fish catch-per-unit-effort (CPUE) was compared for the entire May through August sampling period and spring (May , June) and summer (July , August) seasons separately. There were no significant differences between day and night CPUE at the assemblage level for the entire sampling period or for the spring and summer seasons. However, Hiodon alosoides, Carpiodes/Ictiobus spp. and Macrhybopsis spp. exhibited a diel cycle of abundance within the drift. This pattern was evident although mean Secchi depth (transparency) ranged from 4 to 25 cm during the study and was <30 cm from May through August over the previous nine years. Larval diel drift studies from 48 rivers excluding the Missouri River indicated the primary drift period for larval fishes was at night in 38 rivers and during the day for five, with the remaining rivers showing no pattern. Water transparency was reported for 10 rivers with six being <30 cm or ,low'. Two of these six turbid rivers exhibited significant diel drift patterns. The effect of water transparency on diel drift of larval fishes appears taxa-specific and patterns of abundant taxa could mask patterns of rare taxa when analyzed only at the assemblage level. [source] The distribution,abundance (density) relationship: its form and causes in a tropical mammal order, PrimatesJOURNAL OF BIOGEOGRAPHY, Issue 4 2005A. H. Harcourt Abstract Aim, Across a wide variety of organisms, taxa with high local densities (abundance) have large geographical ranges (distributions). We use primatology's detailed knowledge of its taxon to investigate the form and causes of the relationship in, unusually for macroecological analysis, a tropical taxon. Location, Africa, Central and South America, Asia, Madagascar. Methods, To investigate the form of the density,range relationship, we regressed local density on geographical range size, and also on female body mass, because in the Primates, density correlates strongly with mass. To investigate the biological causes of the relationship, we related (1) abundance (density × range size) and (2) residuals from the density,range regression lines to various measures of (i) resource use, (ii) reproductive rate and (iii) potential specialization. All data are from the literature. Analyses were done at the level of species (n = 140), genera (n = 60) and families/subfamilies (n = 17). We present various levels of results, including for all data, after omission of outlier data, after correction for phylogenetic dependence, and after Bonferroni correction of probabilities for multiple comparisons. Results, Regarding the form of the relationship, Madagascar primates are clear outliers (high densities in small ranges). Among the remaining three realms, the relation of density to range is weak or non-existent at the level of species and genera. However, it is strong, tight and linear at the level of families/subfamilies (r2 = 0.6, F1,10 = 19, P < 0.01). Although among primates, density is very significantly related to mass, at no taxonomic level is range size related to body mass. Consequently, removing the effects of mass makes little to no difference to density,range results. Regarding the biology of the relationship, only traits indicative of specialization are associated with abundance (meaning numbers): rare taxa are more specialized than are abundant taxa. The association is largely via range size, not density. Across families, no traits correlate significantly with the density,range relationship, nor with deviations from it, despite the strength of the relationship at this taxonomic level. Main conclusions, We suggest that in macroecology, analysis at taxonomic levels deeper than that of the relatively ephemeral species can be appropriate. We argue that the several purely methodological explanations for the positive density,range size relationship in primates can be rejected. Of the various biological hypotheses, those having to do with specialization,generalization seem the only applicable ones. The fact that the relationship is entirely via range size, not via density, means that while we might have a biology of range size, we do not yet have one of the density,geographical range relationship. It is probably time to search for multivariate explanations, rather than univariate ones. However, we can for the first time, for at least primates, suggest that any association of abundance or range size with specialization is via the number of different subtaxa, not the average degree of specialization of each subtaxon. The implication for conservation is obvious. [source] Plant regeneration directs changes in grassland composition after extreme drought: a 13-year study in southern SwitzerlandJOURNAL OF ECOLOGY, Issue 4 2004A. STAMPFLI Summary 1The cover of plant species was recorded annually from 1988 to 2000 in nine spatially replicated plots in a species-rich, semi-natural meadow at Negrentino (southern Alps). This period showed large climatic variation and included the centennial maximum and minimum frequency of days with , 10 mm of rain. 2Changes in species composition were compared between three 4-year intervals characterized by increasingly dry weather (1988,91), a preceding extreme drought (1992,95), and increasingly wet weather (1997,2000). Redundancy analysis and anova with repeated spatial replicates were used to find trends in vegetation data across time. 3Recruitment capacity, the potential for fast clonal growth and seasonal expansion rate were determined for abundant taxa and tested in general linear models (GLM) as predictors for rates of change in relative cover of species across the climatically defined 4-year intervals. 4Relative cover of the major growth forms present, graminoids and forbs, changed more in the period following extreme drought than at other times. Recruitment capacity was the only predictor of species' rates of change. 5Following perturbation, re-colonization was the primary driver of vegetation dynamics. The dominant grasses, which lacked high recruitment from seed, therefore decreased in relative abundance. This effect persisted until the end of the study and may represent a lasting response to an extreme climatic event. [source] Coral-reef sounds enable nocturnal navigation by some reef-fish larvae in some places and at some timesJOURNAL OF FISH BIOLOGY, Issue 3 2003J. M. Leis At Lizard Island, Great Barrier Reef, catches of fish larvae by light traps that broadcast nocturnal reef sounds (noisy traps) were compared with catches by quiet traps over two 2ˇ5 week new-moon periods in November (XI) 2000 and January (I) 2001. Three areas were sampled: near-reef (NR, 500 m from the shore) in I, middle (M, 650 m) in I and XI and offshore (O, >1000 m) in XI. The most abundant taxa captured were Apogonidae, Blenniidae, Chaetodontidae, Lethrinidae, Mullidae and Pomacentridae. Significant differences in catch were found between areas, and a position effect was found at the O and M areas. At the NR and M areas, no taxa had significantly greater catches in quiet traps, but larvae of five taxa had significantly greater catches in noisy traps. These were (areas and times of greater catches): Apogonidae (NR; M XI), Mullidae (M I & XI), Pomacentridae (NR; M I & XI), Serranidae (M I) and Sphyraenidae (NR). At the offshore area, five taxa (Apogonidae, Blenniidae, Chaetodontidae, Mullidae and Pomacentridae) had significantly greater catches in quiet traps and only Lethrinidae had significantly greater catches in noisy traps. Thus some taxa (particularly apogonids and pomacentrids which had catches up to 155% greater in noisy traps, but also lethrinids and mullids, and perhaps others), were attracted to reef sounds at night, but this apparently varied with location and time. The sound-enhanced catches imply a radius of attraction of the sound 1ˇ02,1ˇ6 times that of the light. More than 65 m from the speaker,the broadcast sound levels at frequencies typical of fish hearing were equivalent to background levels, providing a maximum radius of sound attraction in this experiment. [source] Community structure and temporal variability of ichthyoplankton in North Brazilian mangrove creeksJOURNAL OF FISH BIOLOGY, Issue 2002A. Barletta-Bergan The species composition and dynamics of fish larvae in three mangrove creeks located in the Caeté Estuary (north Brazil) were studied monthly using a trap net during diurnal ebb tides. A total of 109 954 larvae, representing 25 families and 54 species, were collected from October 1996 to October 1997. The community was dominated numerically by a few species, a feature common for other estuarine fish populations. The most abundant taxa were estuarine species, namely the eleotrid Guavina guavina (46ˇ7%) and the engraulid Anchovia clupeoides (14ˇ9%). The sciaenid Cynoscion acoupa was the only marine species that used the mangroves extensively as a nursery site, occurring mainly at the postflexion stage. The size distribution of G. guavina did not produce shifting modes, indicating continuous transport out of the mangroves by tidal currents. Significantly lower species richness was observed in the late rainy season, primarily due to the emigration of marine species. Intermediate seasons were characterized by more complex larval fish assemblages. The temporal trends of the dominant species was influenced to a great degree by their life history strategy. 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