Validation of a universal set of primers to study animal-associated microeukaryotic communities

The application of metabarcoding to study animal-associated microeukaryotes has been restricted because the universal barcode used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the host. As a result, when host-associated microbial eukaryotes are analysed by metabarcoding, the reads tend to be dominated by host sequences. We have done an in silico validation against the SILVA 18S rRNA database of a non-metazoan primer set (primers that are biased against the metazoan 18S rRNA) that recovers only 2.6% of all the metazoan sequences, while recovering most of the other eukaryotes (80.4%). Among metazoans, the non-metazoan primers are predicted to amplify 74% of Porifera sequences, 4% of Ctenophora, and 15% of Cnidaria, while amplifying almost no sequences within Bilateria. In vivo, these non-metazoan primers reduce significantly the animal signal from coral and human samples, and when compared against universal primers provide at worst a 2-fold decrease in the number of metazoan reads and at best a 2800-fold decrease. This easy, inexpensive, and near-universal method for the study of animal-associated microeukaryotes diversity will contribute to a better understanding of the microbiome.     

Cell-Autonomous Progeroid Changes in Conditional Mouse Models for Repair Endonuclease XPG Deficiency

As part of the Nucleotide Excision Repair (NER) process, the endonuclease XPG is involved in repair of helix-distorting DNA lesions, but the protein has also been implicated in several other DNA repair systems, complicating genotype-phenotype relationship in XPG patients. Defects in XPG can cause either the cancer-prone condition xeroderma pigmentosum (XP) alone, or XP combined with the severe neurodevelopmental disorder Cockayne Syndrome (CS), or the infantile lethal cerebro-oculo-facio-skeletal (COFS) syndrome, characterized by dramatic growth failure, progressive neurodevelopmental abnormalities and greatly reduced life expectancy. Here, we present a novel (conditional) Xpg^−/− mouse model which -in a C57BL6/FVB F1 hybrid genetic background- displays many progeroid features, including cessation of growth, loss of subcutaneous fat, kyphosis, osteoporosis, retinal photoreceptor loss, liver aging, extensive neurodegeneration, and a short lifespan of 4–5 months. We show that deletion of XPG specifically in the liver reproduces the progeroid features in the liver, yet abolishes the effect on growth or lifespan. In addition, specific XPG deletion in neurons and glia of the forebrain creates a progressive neurodegenerative phenotype that shows many characteristics of human XPG deficiency. Our findings therefore exclude that both the liver as well as the neurological phenotype are a secondary consequence of derailment in other cell types, organs or tissues (e.g. vascular abnormalities) and support a cell-autonomous origin caused by the DNA repair defect itself. In addition they allow the dissection of the complex aging process in tissue- and cell-type-specific components. Moreover, our data highlight the critical importance of genetic background in mouse aging studies, establish the Xpg^−/− mouse as a valid model for the severe form of human XPG patients and segmental accelerated aging, and strengthen the link between DNA damage and aging.     

Nitrogen fixation rates in algal turf communities of a degraded versus less degraded coral reef

Algal turf communities are ubiquitous on coral reefs in the Caribbean and are often dominated by N₂-fixing cyanobacteria. However, it is largely unknown (1) how much N₂ is actually fixed by turf communities and (2) which factors affect their N₂ fixation rates. Therefore, we compared N₂ fixation activity by turf communities at different depths and during day and night-time on a degraded versus a less degraded coral reef site on the island of Curaçao. N₂ fixation rates measured with the acetylene reduction assay were slightly higher in shallow (5–10-m depth) than in deep turf communities (30-m depth), and N₂ fixation rates during the daytime significantly exceeded those during the night. N₂ fixation rates by the turf communities did not differ between the degraded and less degraded reef. Both our study and a literature survey of earlier studies indicated that turf communities tend to have lower N₂ fixation rates than cyanobacterial mats. However, at least in our study area, turf communities were more abundant than cyanobacterial mats. Our results therefore suggest that turf communities play an important role in the nitrogen cycle of coral reefs. N₂ fixation by turfs may contribute to an undesirable positive feedback that promotes the proliferation of algal turf communities while accelerating coral reef degradation.     

Early life-history dynamics of Caribbean coral species on artificial substratum: the importance of competition, growth and variation in life-history strategy

The development of a coral community was monitored for 6 years (1998–2004) on 46 m² of artificial settlement substrate in Curaçao, Netherlands Antilles. Growth and survival of recruits (n=1385) belonging to 16 different species were quantified in relation to characteristics of the benthic community developing around them. The early life history dynamics (i.e. growth rate, growth strategy and survival) of corals differed among species although these differences were small for species occupying similar habitats (i.e. underside versus topside of substratum). In contrast to recruit survival, juvenile growth rates were highly variable and unrelated to benthic community structure, at least at the scale of this study. Competing benthic organisms affected coral recruitment success through space preemption (mainly by macroalgae) or recruit overgrowth (mainly by sponges). The results highlight the small spatial scale (mm–cm) at which the processes responsible for recruitment success or failure occur and emphasize the need to include such small-scale observations in studies of coral early life-phase dynamics.     

Crushing behavior of tropical and temperate crabs

The Guamunian xanthids Carpilius maculatus (L.), C. convexus (Forskal), and Eriphia sebana (Shaw & Nodder), and the parthenopid Daldorfia horrida (L.), possess large master claws with molariform teeth than are used to crush the shells of hermit crabs and snails. These crabs typically sever the spire of their prey, or make a gash in the body whorl. They tend to employ sustained pressure on the prey shell, and, except for Eriphia, rarely attack the outer lip, so that the outer lip of the shell typically remains undamaged, except in shells near the critical size, i.e., the maximum size of vulnerability to predation. Temperate species of Cancer (C. productus Randall and C. oregonensi Rathbun) may also crush shelled prey in the larger of their two claws, but more commonly they use both claws together in breaking open their victims. Sustained pressure is applied for only short periods by these crabs.Gastropod adaptations conferring resistance to crushing by crabs include a thick shell, narrow or otherwise small aperture, thickened outer lip, strong sculpture, and a low spire. Emphasis on these traits lowers the critical size of the prey, i.e., permits escape from cushing at a smaller size. An equatorward increase in the expression of the characteristics of crushing-resistance parallels an increase in crushing power of the crabs.     

The ssu locus plays a key role in organosulfur metabolism in Pseudomonas putida S-313

Pseudomonas putida S-313 can utilize a broad range of aromatic sulfonates as sulfur sources for growth in sulfate-free minimal medium. The sulfonates are cleaved monooxygenolytically to yield the corresponding phenols. miniTn5 mutants of strain S-313 which were no longer able to desulfurize arylsulfonates were isolated and were found to carry transposon insertions in the ssuEADCBF operon, which contained genes for an ATP-binding cassette-type transporter (ssuABC), a two-component reduced flavin mononucleotide-dependent monooxygenase (ssuED) closely related to the Escherichia coli alkanesulfonatase, and a protein related to clostridial molybdopterin-binding proteins (ssuF). These mutants were also deficient in growth with a variety of other organosulfur sources, including aromatic and aliphatic sulfate esters, methionine, and aliphatic sulfonates other than the natural sulfonates taurine and cysteate. This pleiotropic phenotype was complemented by the ssu operon, confirming its key role in organosulfur metabolism in this species. Further complementation analysis revealed that the ssuF gene product was required for growth with all of the tested substrates except methionine and that the oxygenase encoded by ssuD was required for growth with sulfonates or methionine. The flavin reductase SsuE was not required for growth with aliphatic sulfonates or methionine but was needed for growth with arylsulfonates, suggesting that an alternative isozyme exists for the former compounds that is not active in transformation of the latter substrates. Aryl sulfate ester utilization was catalyzed by an arylsulfotransferase, and not by an arylsulfatase as in the related species Pseudomonas aeruginosa.     

Shell characters and taxonomy of Latirus and related fasciolariid groups

The neogastropod family Fasciolariidae contains a complex ofgenera related to Latirus Montfort, 1810, many of which havetraits unusual for the family. In a taxonomic revision of someof these genera, based on shell characters, we restrict Latirusto a mainly Indo-West Pacific group of Pliocene to Recent species,which closely resemble the middle Miocene to Recent pantropicalgenus Hemipolygona Rovereto, 1899. Hemipolygona stenomphalus(Habe & Kosuge, 1966) is synonymized with H. recurvirostris(Schubert & Wagner, 1829). Lathyropsis Oostingh, 1939, basedon a small Pliocene species from Indonesia, is here tentativelysubsumed under Polygona Schumacher, 1817. The latter genus,ranging from the late Oligocene to Recent, occurs mainly inthe New World and eastern Atlantic, and contains at least twospecies groups centered on P. infundibulum Schumacher, 1817(type of genus) and P. angulatus (Röding, 1798). Taxa assignedby many authors to Latirulus Cossmann, 1889, are here reassignedto the new genus Turrilatirus (type species: Voluta turritaGmelin, 1791), from the Pliocene to Recent of the Indo-WestPacific. Latirulus is restricted to Eocene species. We assignvarious early Miocene to Recent species from the western Atlanticand eastern Pacific to the new genus Pustulatirus (type species:Latirus mediamericanus, Hertlein & Strong, 1951a). Taxaformerly assigned to Latirus but here removed from Fasciolariidaeinclude Latirus ewekoroensis Adegoke, 1977; the Eocene RusculaCasey, 1904; Lathyrus granifer and L. compactilis, both of Martin,1931; Latirus kirbyi Clark, 1938; Latirus tortilis var. nanafaliusHarris, 1899; and Latirus quercotillaensis Olsson, 1931. (Received 6 September 2005; accepted 29 May 2006)     

Local habitat distribution determines the relative frequency and interbreeding potential for two Caribbean coral morphospecies

We investigate the relationship between habitat heterogeneity and morphological variation in the Caribbean coral species-complex, Madracis pharensis/decactis. This complex showed strong but incomplete morphospecies habitat-matching on a small spatial scale. We find that only one Madracis morphospecies dominates in environments consisting of either few vertical or few horizontal habitats, whereas in environments consisting of a mixture of horizontal and vertical habitats both morphospecies are common. We demonstrate that the observed patterns of morphospecies habitat-matching cannot be explained by a pure polyphenic model, where morphological variants are induced by a genotype-by-environment interaction at their settling site. Instead, we suggest that habitat-matching results in whole or in part from genetically predetermined factors. We present support for the hypothesis that this pattern of habitat-matching is due to habitat- and morphospecies-specific selective factors. Our study describes how a variable environmental factor, i.e. habitat distribution, has a non-linear effect on the spatial distribution of these morphospecies, thereby influencing the genetic organization of the Madracis coral complex at the ~+1–10 km spatial scale.