Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea

The extent of horizontal gene transfer (HGT) among marine pelagic prokaryotes and the role that HGT may have played in their adaptation to this particular environment remain open questions. This is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. Molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of Thaumarchaeota (also known as group I Crenarchaeota) and Euryarchaeota of groups II and III, but only one species (the thaumarchaeote Candidatus Nitrosopumilus maritimus) has been isolated in pure culture so far. Therefore, metagenomics remains the most powerful approach to study these environmental groups. To investigate the impact of HGT in marine archaea, we carried out detailed phylogenetic analyses of all open reading frames of 21 archaeal 16S rRNA gene-containing fosmids and, to extend our analysis to other genomic regions, also of fosmid-end sequences of 12 774 fosmids from three different deep-sea locations (South Atlantic and Adriatic Sea at 1000 m depth, and Ionian Sea at 3000 m depth). We found high HGT rates in both marine planktonic Thaumarchaeota and Euryarchaeota, with remarkable converging values estimated from complete-fosmid and fosmid-end sequence analysis (25 and 21% of the genes, respectively). Most HGTs came from bacterial donors (mainly from Proteobacteria, Firmicutes and Chloroflexi) but also from other archaea and eukaryotes. Phylogenetic analyses showed that in most cases HGTs are shared by several representatives of the studied groups, implying that they are ancient and have been conserved over relatively long evolutionary periods. This, together with the functions carried out by these acquired genes (mostly related to energy metabolism and transport of metabolites across membranes), suggests that HGT has played an important role in the adaptation of these archaea to the cold and nutrient-depleted deep marine environment.     

A radiative transfer modeling approach for accurate interpretation of PAM fluorometry experiments in suspended algal cultures

The results of a numerical study on the simulation of pulse amplitude modulated (PAM) fluorometry within dense suspensions of photosynthetic microorganisms are presented. The Monte Carlo method was used to solve the radiative transfer equation in an algae‐filled cuvette, taking into account absorption, anisotropic scattering, and fluorescence, as well as Fresnel reflections at interfaces. This method was used to simulate the transport of excitation and fluorescence light in a common laboratory fluorometer. In this fluorometer, detected fluorescence originates from a multitude of locations within the algal suspension, which can be exposed to very different fluence rates. The fluorescence‐weighted fluence rate is reported, which is the local fluence rate of actinic light, averaged over all locations from which detected fluorescence originated. A methodology is reported for recovering the fluorescence‐weighted fluence rate as a function of the transmittance of measuring light and actinic light through the sample, which are easily measured with common laboratory fluorometers. The fluorescence‐weighted fluence rate can in turn be used as a correction factor for recovering intrinsic physiological parameters, such as the functional cross section of Photosystem II, from apparent (experimental) values. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1601–1615, 2016     

MORPHOLOGY AND TAXONOMY OF PROROCENTRUM MEXICANUM AND REINSTATEMENT OF PROROCENTRUM RHATHYMUM (DINOPHYCEAE)1

Dinoflagellates collected during red tide events in Bahia Mazatlan, Mexico during the early spring of 1999 and 2000 appeared under LM to belong to Prorocentrum mexicanum Osorio‐Tafall. Observations with SEM of those populations showed marked differences in shape and microornamentation from the related species, Prorocentrum rhathymum Loeblich III, Sherley and Schmidt. In P. mexicanum, the presence and dimensions of poroids, the uneven distribution of trichocyst pores not located in depressions, and the general architecture of the periflagellar region are more closely related to Prorocentrum caribbaeum Faust. Also, P. mexicanum has a three‐horned (sometimes two‐horned) spine and is deeper in the anterior than the posterior region, whereas P. rhathymum has a simple small spine and its sagittal view is oval. Furthermore, the number and distribution of trichocyst pores in the periflagellar area is different between the two species, being located on both valves in P. mexicanum and only on the right valve in P. rhathymum. To date, true P. mexicanum has been described only from plankton sampling, whereas P. rhathymum was frequently mentioned associated with floating detritus (macroalgae) but also forming red tides. Altogether, the evidence presented demonstrates that P. mexicanum (planktonic) and P. rhathymum (epibenthic) are distinct species and are not synonyms, as is often accepted.     

Paleoceanographic implications of smaller benthic and planktonic foraminifera from the Eocene Pazin Basin (Coastal Dinarides,Croatia)

Summary Smaller benthic and planktonic foraminifera from the clastic sediments of the Pazin Basin (Istria, Croatia) were studied in order to obtain more data about paleoceanographic conditions that existed in the Middle Eocene Dinaric foreland basin. The succession investigated corresponds to the Middle Eocene planktonic foraminiferal zones Globigerapsis kugleri/Morozovella aragonensis (P11), Morozovella lehneri (P12), and Globigerapsis beckmanni (P13). Benthic foraminiferal assemblages from the clastic succession are dominated by epifaunal trochospiral genera suggesting oligotrophic to mesotrophic conditions and moderately oxygenated bottom waters. Planktonic foraminiferal assemblages indicate mesotrophic to eutrophic conditions of the surface waters, with increased eutrophication in the upper part of the section. Water depth, based on the ratio between planktonic and epifaunal benthic foraminifera and on the recognized species of cosmopolitan benthic foraminifera, was estimated to have been between about 900 and 1200 m. The basin was elongated and open to marine currents on both sides allowing good circulation and ventilation of the bottom water.     

How landscapes affect the evolution of dispersal behaviour in reef fishes: results from an individual‐based model

The vast majority of tropical reef fishes have a sedentary adult phase and pelagic larval phase that is potentially highly dispersive. Dispersal may be favoured by a wide range of factors including the arrangement of suitable habitat in space. In this paper the dispersal strategy of individuals is followed and allowed to evolve in a simplified model of three different landscapes: an enclosed sea, an open archipelago and a barrier reef. The three landscapes have very different characteristics, but all have similar spatial clumping of reef habitat. In all landscapes, as minimum time to settlement increases, evolved movement strategy also increases and longer settlement windows favour dispersal. In the archipelago movement is not maximized until the minimum pelagic duration is longer than in the other landscapes. The model predicts that, given the same pelagic duration, species from enclosed seas should have more dispersive behaviours than those from open archipelagos, because of the density of habitat and the aggregation of habitat in space affect the likelihood of larvae finding suitable habitat for settlement.     

海南岛西北沿岸海域浮游桡足类的分布及群落特征

为了解昌江沿岸海域生态系统的现状, 探讨海域环境因素对浮游动物的生存环境造成的影响。本文根据2008年11月至2009年7月在海南西部昌江沿岸水域21个测站、4个季度月调查所获的浮游桡足类样品数据, 对该海域浮游桡足类群落结构、分布、季节变化及影响因素进行了分析。本调查共鉴定出桡足类44种, 隶属4目17科24属, 其中秋季25种, 冬季23种, 春季22种, 夏季23种。本次调查共发现优势种6种, 分别是微刺哲水蚤(Canthocalanus pauper)、亚强次真哲水蚤(Subeucalanus subcrassus)、锥形宽水蚤(Temora turbinata)、刺尾纺锤水蚤(Acartia spinicauda)、椭形长足水蚤(Calanopia elliptica)和精致真刺水蚤(Euchaeta concinna), 优势种以近岸暖水种居多。浮游桡足类丰度季节变化明显: 冬季最高, 达409 ind./m³; 秋季次之, 为144 ind./m³, 春季为55 ind./m³, 夏季最低仅为17 ind./m³。其丰度的平面分布显示: 秋、冬季节分别在海区中部和南部形成明显密集区, 春、夏季节则大致呈现由外海向近岸逐渐递减的趋势。浮游桡足类的多样性指数(H')表现为夏季>春季>秋季>冬季, 春、夏季的均匀度指数(J')明显高于秋、冬季。本调查反映出该海区的桡足类群落具有热带—亚热带区系特征, 种类组成季节更替明显, 桡足类种群受海域水温和硅藻的影响明显, 受盐度影响不明显。     

Copepod nauplii from the barrier reef of Belize

A study of areal distribution of the copepod nauplii near mangrove covered cays on the barrier reef of Belize was begun in the summer of 1989 and continued in the spring of 1990 with the collection of twenty samples from four locations. At distances in the order of 100 of meters to 1000 from the mangrove prop roots there were thousands of nauplii m^–3. In the samples from Twin Cays where the plankton tows were made 15 m from the prop roots or less the average was 387 nauplii m^–3. Copepod nauplii compose 60% of the metazoan plankton abundance in all of the samples. Harpacticoid nauplii were the largest single component of the plankton in every sample; they account for 42% to 76% of the copepod nauplii. Cyclopoid nauplii represent 13 to 40% and are second to the harpacticoid nauplii. Calanoid nauplii account for 2% to 23% of the copepod nauplii.     

2010年两个航次獐子岛海域浮游纤毛虫丰度和生物量

2010年7、8月在北黄海獐子岛海域进行了浮游纤毛虫丰度和生物量的调查。7月浮游纤毛虫的平均丰度为(5107±4451) 个/L,平均生物量为(10.17±9.06) μg C/L。8月浮游纤毛虫的平均丰度为(7894±7212) 个/L,平均生物量为(15.24±18.49) μg C/L。7月表层浮游纤毛虫丰度和生物量均呈现近岸多、远岸少的趋势。8月Y1-3、Y2-5两个站表层纤毛虫丰度较高,Y2-5、Y1-1两个站表层纤毛虫生物量较高。7月STA断面浮游纤毛虫丰度呈现表层或次表层高、底层低的特点。8月STA、Y1断面纤毛虫丰度在表层或次表层高、底层低,而Y2断面纤毛虫垂直分布较一致。7月纤毛虫水体丰度及生物量在近岸较远岸高, 8月纤毛虫水体丰度及生物量在离岛较近的Y2-5、Y1-1两站较高。7、8月航次中分别鉴定出砂壳纤毛虫17和21种,其中拟铃虫属(Tintinnopsis)种数最多,Tintinnopsis corniger Hada, 1964为中国海区的新记录种。7、8月砂壳纤毛虫丰度占纤毛虫总丰度的平均比例分别为(19.0±21.6)%和(13.0±16.1)%;7、8月砂壳纤毛虫生物量占纤毛虫总生物量的平均比例分别为(58.2±33.0)%和(42.6±33.2)%。7、8月两个航次中小型无壳纤毛虫在无壳纤毛虫丰度中均占绝对优势。     

Climate-driven genetic divergence of limpets with different life histories across a southeast African marine biogeographic disjunction: different processes, same outcome

Genetic divergence among populations of marine broadcast spawners in the absence of past geological barriers presents an intriguing challenge to understanding speciation in the sea. To determine how differences in life history affect genetic divergence and demographic histories across incomplete dispersal barriers, we conducted a comparative phylogeographic study of three intertidal limpets (Siphonaria spp.) represented on either side of a biogeographic disjunction separating tropical and subtropical marine provinces in southeastern Africa. Using a combination of mitochondrial and nuclear sequence data, we identified two distinct evolutionary lineages each in both Siphonaria concinna (a planktonic disperser) and S. nigerrima (a direct developer), and panmixia in a second planktonic disperser, S. capensis. Although phylogeographic breaks were present in two species, how these became established differed depending on their life histories. In the direct developer, lack of gene flow following divergence, and demographic expansion from a small initial size in the species' subtropical population, point to a single colonisation event. In contrast, the evolutionary lineages of the planktonic disperser split into two genetic lineages with much larger initial population sizes and southward gene flow continued at least periodically, indicating that divergence in this species may have been driven by a combination of reduced larval dispersal and divergent selection. These findings help explain why the presence or absence of phylogeographic breaks often appears to be independent of species' dispersal potential.