Field of Science

The Philosopher's Bacterium

Picture the mediaeval alchemist, standing before a smoking crucible, adding ingredients and performing the requisite incantations. Eventually, he allows the crucible to cool so that he might examine the results. Has he succeeded? Has he achieved his goal of extracting pure gold from the base earth? Alas, he has not*, because he is only human, and he lacks the powers of a Geovibrio.

*For which we should perhaps be grateful. To quote King Midas in an episode of Concrete Cow, "I really should have foreseen the inflationary effect of all that new gold on our economy".

Deferribacter desulfuricans, photographed by K. Takai.

Geovibrio ferrirudecens is a species belonging to the 'phylum' Deferribacteres, an assemblage of Gram-negative bacteria known as yet from only a small number of species. However, the known species are all quite ecologically disparate, so we may have only scratched the surface of deferribacterial diversity. All are anaerobic organotrophs, utilising various organic compounds as electron donors in respiration*. Species vary in their temperature preferences from mesophily (growing at 'room temperature') to moderate thermophily (up to about 60°C). Cells may be immobile rods, or they may be motile with a single polar flagellum (bipolar flagella have been observed in Denitrovibrio acetiphilus, indicating reproduction by budding). Cells of Geovibrio, at least, can occur in chains as well as individually. Known habitats of Deferribacteres include water in oil reservoirs for Deferribacter thermophilus (Garrity & Holt 2001), Japanese hot springs for Calditerrivibrio nitroreducens (Iino et al. 2008), hydrocarbon-contaminated soils for Geovibrio ferrireducens (Garrity & Holt 2001), and the epithelial lining of a mouse intestine for Mucispirillum schaedleri (Robertson et al. 2005). With regard to this last genus, it stands as a good example of how poor is our understanding of real bacterial diversity that a significant component of the intestinal flora of a major model organism was not identified until 2005! When people express surprise to me that there are still new species of organism to be described in the world, I inform them that, at the microbial level, there are almost certainly undescribed species living on you right now.

*As do we, of course. If you remember your high school biology, you'll recall that human respiration reacts glucose and oxygen to produce carbon dioxide and water. In this reaction, glucose is the electron donor while oxygen is the electron receptor.

Geovibrio ferrireducens with periplasmic gold deposits, from Kashefi et al. (2001).

Species of Deferribacteres also vary in their preferred electron receptors. Calditerrivibrio nitroreducens, as indicated by its species name, reduces nitrate, converting it into ammonium. The very recently described Seleniivibrio woodruffii utilises selenium and arsenic compounds (Rauschenbach et al. 2013; arsenate-respiring bacteria can be significant to public health as they convert arsenates to more soluble arsenites, causing arsenic to leach into groundwater). Deferribacter thermophilus and Geovibrio ferrireducens each received part of their names because they grow off ferric iron (Fe3+), converting it into ferrous iron (Fe2+). Ferrous iron is much more soluble than ferric iron, so iron-reducing bacteria can cause corrosion to iron structures. Both these taxa may also use other electron acceptors. Deferribacter can grow off manganese(IV) or nitrate. Geovibrio doesn't reduce either of those substances, but it has been shown that it can use hydrogen as an electron donor to reduce soluble gold(III) to elemental gold, which becomes deposited in the periplasmic space between the cell membranes (Kashefi et al. 2001). Geovibrio is only one of a number of bacteria that can pull off this trick, and it has been bacteria may have been responsible for the creation of many of the world's gold deposits. When the alchemist of our opening paragraph was struggling with his proto-chemistry, he should have been examining his biology.


Garrity, G. M., & J. G. Holt. 2001. Phylum BIX. Deferribacteres phy. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd ed., vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria (Boone, D. R., R. W. Castenholz & G. M. Garrity, eds) pp. 465-471. Springer.

Iino, T., T. Nakagawa, K. Mori, S. Harayama & K. Suzuki. 2008. Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan. International Journal of Systematic and Evolutionary Microbiology 58: 1675-1679.

Kashefi, K., J. M. Tor, K. P. Nevin & D. R. Lovley. 2001. Reductive precipitation of gold by dissimilatory Fe(III)-reducing Bacteria and Archaea. Applied and Environmental Microbiology 67 (7): 3275-2279.

Rauschenbach, I., V. Posternak, P. Cantarella, J. McConnell, V. Starovoytov & M. M. Häggblom (in press, 2013) Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae. International Journal of Systematic and Evolutionary Microbiology.

Robertson, B. R., J. L. O’Rourke, B. A. Neilan, P. Vandamme, S. L. W. On, J. G. Fox & Adrian Lee. 2005. Mucispirillum schaedleri gen. nov., sp. nov., a spiral-shaped bacterium colonizing the mucus layer of the gastrointestinal tract of laboratory rodents. International Journal of Systematic and Evolutionary Microbiology 55: 1199-1204.

Why Are There So Many Avahis?

Western woolly lemur Avahi occidentalis, photographed by Axeltelford.

A few years back, I wrote a post on the lemur family Indriidae: the indri, the avahis, the sifakas. One thing I briefly mentioned in that post is that recent years have seen an apparent avalanche of new indriid species being described. But why has this happened, and how sturdy are these new distinctions?

In 1982, Tattersall provided an overview of Malagasy lemurs that recognised just four species of indriid: the indri Indri indri, the avahi Avahi laniger, Verreaux's sifaka Propithecus verreauxi and the diademed sifaka P. diadema (Tattersall 2007). A fifth species was added in 2008, the golden-crowned sifaka P. tattersalli. But the real explosion has come in only the last ten years or so. Recent workers have proposed the recognition of seven species of sifaka (Mayor et al. 2004), and no less than nine species of avahi (Zaramody et al. 2006, Andriantompohavana et al. 2007, Lei et al. 2008). Each of the species within a genus is generally geographically separated from its congeners, and some species are recorded only from very small ranges.

In the case of the sifakas, none of the new 'species' is actually a new taxonomic entity per se. With the exception of P. tattersalli, all were previously recognised previously as subspecies of either P. verreauxi or P. diadema. The most obvious differences between the various varieties of sifaka is coloration. As noted in the earlier post linked to above, popular depictions of sifakas are heavily biased towards P. [verreauxi] verreauxi, found in the south-west of Madagascar, with a white body and black skull-cap (photo below by Jouan & Rius):

However, the sifakas are much more varied than you might think from watching David Attenborough documentaries alone. As well as the red-and-black Propithecus [diadema] diadema illustrated in the earlier post, sifakas vary from the almost entirely black P. [diadema] perrieri of the far north of Madagascar (photograph by Pete Oxford):

to the almost entirely white north-eastern P. [diadema] candidus (photo by Kevin Schafer):

The various sifaka subspecies were analysed by Mayor et al. (2004), who identified them as genetically distinct as well as distinct in appearance, and therefore recommended treating them all as separate species. However, other authors such as Tattersall (2007) have pointed out that morphological distinctions between populations may become less clear when overall variation is considered.
The above photos, from Rakotonirina et al. (2013), show variation in sifakas at a single site in central-west Madagascar, near the boundary between the ranges of Propithecus [verreauxi] deckeni and P. [verreauxi] coronatus and including individuals that might be assigned on grounds of coloration to either taxon.

In the case of the avahis, things are even more convoluted than for the sifakas. While the diurnal sifakas may vary noticeably in external appearance, the nocturnal avahis keep to a more or less basic brown. There are some slight differences between avahis on the western and eastern sides of Madagascar that had lead to the recognition of two separate subspecies, Avahi laniger laniger in the east and A. l. occidentalis in the west. A. laniger and A. occidentalis were subsequently treated as separate species on the basis of differences in their karyotypes. Each has been further subdivided into multiple species largely on the basis of genetic data alone (though vocalisation data was also a factor in separating A. unicolor from A. occidentalis). What is more, the genetic distinctions have mostly been made on the basis of mitochondrial data only, and some 'species' have only been represented in analyses by data from a few individuals. Markolf et al. (2011) suggested that genetic species could not be distinguished reliably on the basis of such small samples because of the increased risk of confusing individual variation for species-level distinctions. In the majority of cases, differences in mitochondrial genes between Avahi samples have correlated with geographical separation, but there is at least one notable exception. The central-east Malagasy location of Ranomafana has provided samples that fall into three distinct haplotype clusters. Though recognised as a single species A. peyrierasi on the basis of their common distribution, these three clusters do not form a monophyletic group in phylogenetic analyses, and the geographically separate taxa A. betsileo, A. meridionalis and A. ramanantsoavana are all nested between the A. peyrierasi haplotypes (Lei et al. 2008).

Eastern woolly lemur Avahi laniger, photographed by Inaki Relanzon.

None of the Avahi species as currently recognised overlap in range. However, in a landmass that has lost four-fifths or more of its original forest cover, it is worth asking how much of this isolation is original, and how much man-made relictualism. As always in questions of scientific research, we are left noting that further investigation is required.


Andriantompohavana, R., R. Lei, J. R. Zaonarivelo, S. E. Engberg, G. Nalanirina, S. M. McGuire, G. D. Shore, J. Andrianasolo, K. Herrington, R. A. Brenneman & E. E. Louis Jr. 2007. Molecular phylogeny and taxonomic revision of the woolly lemurs, genus Avahi (Primates: Lemuriformes). Special Publications, Museum of Texas Tech University 51: 1-59.

Lei, R., S. E. Engberg, R. Andriantompohavana, S. M. McGuire, R. A. Mittermeier, J. R. Zaonarivelo, R. A. Brenneman & E. E. Louis. 2008. Nocturnal lemur diversity at Masoala National Park. Special Publications, Museum of Texas Tech University 53: 1-41.

Markolf, M., M. Brameier & P. M. Kappeler. 2011. On species delimitation: yet another lemur species or just genetic variation? BMC Evolutionary Biology 11: 216.

Mayor, M. I., J. A. Sommer, M. L. Houck, J. R. Zaonarivelo, P. C. Wright, C. Ingram, S. R. Engel & E. E. Louis Jr. 2004. Specific status of Propithecus spp. International Journal of Primatology 25 (4): 875-900.

Rakotonirina, L. H. F., F. Randriantsara, A. H. Rakotoarisoa, R. Rakotondrabe, J. Razafindramanana, J. Ratsimbazafy & T. King (in press, 2013). A preliminary assessment of sifaka (Propithecus) distribution, chromatic variation and conservation in western central Madagascar. Primate Conservation.

Tattersall, I. 2007. Madagascar's lemurs: cryptic diversity or taxonomic inflation? Evolutionary Anthropology 16: 12-23.

Zaramody, A., J.-L. Fausser, C. Roos, D. Zinner, N. Andriaholinirina, C. Rabarivola, I. Norscia, I. Tattersall & Y. Rumpler. 2006. Molecular phylogeny and taxonomic revision of the eastern woolly lemurs (Avahi laniger). Primate Report 74: 9-23.

Bye, Bye, Spinicrus

Female, sorry, Megalopsalis nigricans, photographed by Tony.

I've just had a paper out. The funny thing is, it's making me feel both pleased yet a little maudlin, because it represents something of an end of an era. The last part of my PhD thesis has been published. The last remnant of my student days has been cast off. I think I need a hug.

The paper in question is: Taylor, C. K. 2013. Further revision of the genus Megalopsalis (Opiliones, Neopilionidae), with the description of seven new species. ZooKeys 328: 59-117. It's open access, so go take a squizz. One thing that I also can't resist pointing out, though I don't know if it really makes much difference because it's a primarily online journal and hardly anyone will see the print issue: it's one of my images on the cover.

Technically, this paper represents my long-awaited (by me, at least) revision of the harvestman genus Spinicrus. In the end, though, I had to change the title of the paper, because on of the main results of this revision was that Spinicrus became a synonym of the older genus Megalopsalis. In an earlier publication, I cut Megalopsalis down to size by removing its New Zealand species to a new genus, Forsteropsalis. But now it's back, and stronger than ever before!
Female Megalopsalis tasmanica, the erstwhile Spinicrus tasmanicum. Another photograph from Tony.

Previously, Spinicrus was primarily separated from Megalopsalis by one feature: the presence of a side branch on one of the segments of the pedipalps of Megalopsalis. Taxonomists tend to be wary of defining a group purely by the absence of features. It implies that the members of that group are united more by the idea that they just don't belong in any other group, rather than anything that actually connects them per se. So, in this case, Megalopsalis was the species with a pedipalp side-branch, and Spinicrus was... the rest. It also didn't help matters that a pedipalp side-branch is something that has evolved and de-evolved a number of times within harvestmen, leading to a bit of questioning about its significance. A few years ago, I separated a few of the more distinctive 'Spinicrus' as the genus Neopantopsalis. This made Spinicrus a bit less heterogeneous but still didn't solve the underlying issue. It just meant that now you took out Megalopsalis and took out Neopantopsalis, and Spinicrus was still... the rest.

The answer, as so often in invertebrate taxonomy, came largely from the boy bits. When I looked at the male genitalia, I found that Megalopsalis and Spinicrus species shared a similar penis morphology, in which the end of the penis was fairly short, flat and shaped more or less like a rounded triangle:
This is what a 'Spinicrus' stewarti penis looks like.

In contrast, the end of the penis in Neopantopsalis species is longer, as demonstrated by N. thaumatopoios:

Put these features into a phylogeny of the family that these genera belong to (Neopilionidae), and I overall ended up with this:
Consensus of various phylogenetic analyses under various parameters (numbers at nodes represent the percentage of analyses in which that clade was recovered). Taxa coloured green are what would have been called 'Spinicrus' previously, while those in red would have been 'Megalopsalis'.

Note that this is a bit of a faux phylogeny, because it's a comparative summary of separate analyses under separate parameters (see the paper for details). Only those clades marked with a 100 were supported in all analyses. The important detail is the distribution of the green 'Spinicrus' relative to the red 'Megalopsalis': no matter what the analytical conditions, 'Megalopsalis' was always nested well within 'Spinicrus'. Indeed, under most conditions, 'Megalopsalis' was polyphyletic within 'Spinicrus'. Because of this, and because of the lack of any positive uniting features for Spinicrus species that were not also present in Megalopsalis, I felt the best course of action was to declare the two genera synonyms. Also subsumed under Megalopsalis was Hypomegalopsalis, a species that I had earlier established for a single species of uncertain affinities (Megalopsalis tanisphyros in the tree above). At the time, I commented that, "if anyone conducts a further study in the future that supports quashing Hypomegalopsalis, I won't be protesting". The fact that I got to do that myself just makes me all the happier.

There's a lot more I could talk about here, but I'm sure you all stopped reading long ago. Just go to the paper.

The Antedoninae: (Relatively) Big-Bellied Feather Stars

Several individuals of Antedon bifida attached to a kelp stipe, photographed by Bernard Picton.

The feather stars and other crinoids are both the most divergent and least known of the modern echinoderms. This is the second post here at Catalogue of Organisms on modern feather stars; an earlier post gave a brief overview of some of the details of the feather star lifestyle and anatomy. The main subject of the earlier post was the family Charitometridae; this post will focus on a different group, the Antedoninae. Yes, Virginia, there are different varieties of feather star.

The Antedonidae and related families differ from most other feather stars in that the internal cavity of the centrodorsal, the plate that forms the base of the calyx (central cup) of the feather star, is relatively large compared to the centrodorsal's diameter (in life, this cavity has organs nestled in it). When the antedonids were reviewed by the American echinodermatologist Austin H. Clark (Clark & Clark 1957*), he regarded this difference as significant enough to treat the antedonids and related families as a separate group, the Macrophreata, from other families in the Oligophreata with only a small centrodorsal cavity. However, later researchers have downplayed the significance of this distinction (e.g. Wienberg Rasmussen 1978), and even the monophyly of the Antedonidae has been questioned. Well-developed muscular articulations in the upper part of the calyx also indicate that antedonids are generally stronger swimmers than other feather stars (Meyer 1972). Clark & Clark (1967) divided the antedonids between six subfamilies, but Ailsa Clark commented that the distinctions between subfamilies were not always clear.

*Austin Clark's epic revision of the living crinoids was left incomplete after his death in 1954, until it was taken up by the British researcher Ailsa Clark (no relation, as far as I've found). The section of Clark's monograph on the 'Macrophreata' therefore made its debut under both researcher's names.

Specimen of Dorometra photographed by Lyle Vail and Anne Hoggett. The page linked notes that this species swims actively when disturbed, before 'holding their arms above the disk to form a shuttlecock shape and then plummeting towards the bottom'.

The Antedoninae generally differ from other antedonids in having rather short cirri (though the Philippine species Eumetra chamberlaini has exceptionally long cirri, up to about a third of the length of its arms). The cirri are also rounded dorsally, without dorsal spines or ridges, and most species lack ventral spines except one on the penultimate segment of the cirrus that opposes the terminal claw. The centrodorsal is low and rounded in the majority of species, though it may become raised and closer to conical. Antedonines include some of the shallowest-living of recent crinoids, with some species even found in tide pools; the deepest-living antedonines are known from 932 m. Clark and Clark (1967) recognised ten genera within the Antedoninae; a fossil genus Palaeantedon (from the Eocene to Quaternary) was listed in addition to the Recent genera by Wienberg Rasmussen (1978), and an eleventh Recent genus Ctenantedon was described by Meyer (1972).

The rosy feather star Antedon bifida and the Mediterranean feather star A. mediterranea are among the best-studied of all feather stars, primarily due to both being found in shallow waters around Europe. However, the greater diversity of antedonines is known from the Indo-Pacific. Apart from species of Antedon, the only Recent antedonine known from the Atlantic is the Caribbean Ctenantedon kinziei (the fossil species of Palaeantedon are also Atlantic). Characters used to distinguish genera include features of the pinnules, the slender side-branches of the arms. Antedon species, for instance, usually have the second and third pinnules on each arm similar in size to each other, and both distinctly shorter than the first pinnule. Ctenantedon kinziei is unusual in having a comb of 'teeth' developed in the distal part of the proximal pinnules. The function of these teeth is not entirely certain, though Meyer (1972) noted that he had observed the oral pinnules of comasterid feather stars (which also bear similar teeth) moving in and out from the central disk in a manner that suggested they were being used to remove undigested food and other waste material.


Clark, A. H., & A. M. Clark. 1967. A monograph of the living crinoids. Volume 1. The comatulids. Part 5—suborders Oligophreata (concluded) and Macrophreata. Smithsonian Institution, United States National Museum, Bulletin 82.

Meyer, D. L. 1972. Ctenantedon, a new antedonid crinoid convergent with comasterids. Bulletin of Marine Science 22 (1): 53-66.

Wienberg Rasmussen, H. 1978. Articulata. In Treatise on Invertebrate Paleontology pt. T. Echinodermata 2. Crinoidea (R. C. Moore & C. Teichert, eds) vol. 3 pp. T813-T927. The Geological Society of America, Inc.: Boulder (Colorado), and The University of Kansas: Lawrence (Kansas).