Field of Science

What Value a Sporangium?

Regular readers of this site will know that I select the subject of most posts by assigning myself a taxon semi-randomly and then trying to find something to say about it. And sometimes when I spin the wheel, what comes out can be a little obscure. It's time for another entry in "Taxon Names that No-one Uses"!

Colony of Dimargaris cristalligena (Dimargaritaceae), from here.


As far as I can tell, the name 'Meromycetidae' has been used in the literature once, and once only. In 1998, Tom Cavalier-Smith coined it as a label for a subclass of fungi in his "Revised six-kingdom system of life". Even compared to other fungal classifications current at the time, Cavalier-Smith's system for fungi contained a lot of features that seemed a little odd (Laboulbeniales as trichomycetes?) and most of his novel propositions were to subsequently sink without a trace. The 'Meromycetidae' were intended to be a subgroup of what most other authors of the time would have called the 'zygomycetes'. Zygomycetes, as generally recognised, were mostly microscopic fungi that lack the dikaryotic phase* of more familiar macrofungi such as mushrooms, and lack the flagellated spores of other microscopic fungi. The most familiar zygomycetes are various household moulds. It is now well established, however, that 'zygomycetes' are a non-monophyletic grade within fungal evolution, leading to their dissolution as a formal class though one may still encounter the name being used informally for convenience.

*A period in the reproductive life cycle of many fungi where the nuclei from two parents have entered a single cell, but continue to function and divide separately without yet fusing to form a daughter nucleus.

Mature sporangiophore of Syncephalastrum racemosum, showing merosporangia radiating from central vesicle. Copyright George Barron.


It is not always easy to tell how Cavalier-Smith's (1998) taxa were supposed to be applied, but it seems evident that the Meromycetidae were intended to cover those zygomycetes that produced merosporangia. Merosporangia are elongate sporangia that may contain one to several asexually-produced spores in series. In a review of fungi with merosporangia, Benjamin (1966) identified four groups that might be described as possessing such structures: Syncephalastrum, Piptocephalidaceae, Kickxellaceae and Dimargaritaceae. Syncephalastrum and the Kickxellaceae are minute soil saprobes; the Piptocephalidaceae and Dimargaritaceae are parasites of other fungi, mostly of other zygomycetes. However, Bejamin noted that the differences between these groups were such that only the Kickxellaceae and Dimargaritaceae could be considered as likely to be related to each other. The others differed in features of their hyphal structure, and also in details of how their merosporangia developed. More recent molecular studies have sided with Benjamin rather than with Cavalier-Smith: the production of a merosporangium does not tally with a single ancestry, and the various merosporangium-producing fungi can be placed in quite distinct lineages.

Young sporangiophore of Syncephalis nodosa, a representative of the Piptocephalidaceae. Copyright George Barron.


Syncephalastrum, for instance, belongs to the Mucorales, in the same fungal order as the house moulds Mucor and Rhizopus. This tallies with the observation by Benjamin that, but for its unusual sporangia, Syncephalastrum could be considered a fairly typical member of that group. The Piptocephalidaceae belong to the Zoopagales, other members of which are also parasites or predators, attacking minute animals such as nematodes or protozoa such as amoebae.

Comparative diagrams of sporangiophores of Coemansia (Kickxellaceae) and Smittium (Harpellales), showing similarities in overall structure, from Moss & Young (1978).


The Kickxellaceae and Dimargaritaceae together belong to a recently recognised fungal group dubbed the Kickxellomycotina, all members of which share a hyphal structure that is unique among fungi. Whereas other 'zygomycetes' have the hyphae more or less coenocytic (without regular division into cells), Kickxellomycotina have the hyphae divided by regular septa. The septa each contain a disciform pore that is sealed by a lenticular plug. This group also includes two other orders of fungi, the Harpellales and Asellariales, that have been referred to in the past as the trichomycetes. Members of these two orders are symbionts in the guts of arthropods, usually in aquatic or damp habitats. Their reproductive structures are very similar to those of Kickxellaceae, with single-spored sporangia developing as side branches of a septate sporangiophore. Indeed, if Kickxellaceae are to be described as producing merosporangia, then Harpellales and Asellariales should as well. Molecular phylogenetic analyses also support a close relationship between these three groups to the exclusion of the more distinctive Dimargaritaceae (Tretter et al. 2014).

Diagrams of sporangiophores and merosporangia of Dimargaris arida (Dimargaritaceae), from here.


The higher relationships of the various 'zygomycete' subgroups are still being investigated. It is fairly well established at this point that no close relationship exists between Syncephalastrum in the Mucorales and the other merosporangial fungi. A number of analyses, on the other hand, have suggested some sort of relationship between the Kickxellomycotina and the Zoopagales, but so far only with low support. Because the organisms involved are so derived, and have possible undergone fairly rapid rates of evolution, mycologists have been reluctant to read too much into these analyses, and new hypotheses may be yet to come.

REFERENCES

Benjamin, R. K. 1966. The merosporangium. Mycologia 58 (1): 1–42.

Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biological Reviews 73: 203–208.

Tretter, E. D., E. M. Johnson, G. L. Benny, R. W. Lichtwardt, Y. Wang, P. Kandel, S. J. Novak, J. F. Smith & M. M. White. 2014. An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales. Mycologia 106 (5): 912–935.

The Green Sulphur Bacteria

There was a time when we really didn't know what to make of bacterial systematics. We knew that there were a lot of different species out there (not, it turns out, any near as many as there actually are, but still...) but prior to the molecular revolution of the last few decades we lacked the facilities to tell how many of them were related to each other. Nevertheless, there are some bacterial groupings that are distinctive enough to have been recognised even before the advent of regular genetic sequencing. One such group is the green sulphur bacteria.

Culture of Chlorobium phaeobacteroides, from here.


Two things must you know of green sulphur bacteria. One, they are (commonly) green. Two, they are associated with sulphur. Like the more familiar blue-green algae, green sulphur bacteria are photosynthetic, using light energy collected by coloured pigments to assimilate carbon dioxide. In some species the photosynthetic pigments are bacteriochlorophyll c or d, giving the cells a grass green coloration. In others, the pigment is bacteriochlorophyll e, and the cells are a chocolate brown. In contrast to blue-green algae, green sulphur bacteria are anaerobic: instead of using water as an electron donor to produce oxygen, they oxidise sulphide or sulphur to produce sulphur or sulphate (a single species, C. ferrooxidans, uses ferrous iron instead of sulphur). As a result, they are found growing in habitats that light reaches but oxygen doesn't. Many species are found in thermally stratified lakes or brackish lagoons with little mixing between upper and lower water layers, and form a distinct planktonic layer at the optimum intersection between light and sulphide gradients. They are also common in sulphur-rich hot springs. The cell's bacteriochlorophylls are concentrated into structures referred to as chlorosomes attached to the cytoplasmic membrane, maximising their ability to gather light at the low intensities. A number of species contain gas vacuoles to improve buoyancy. Most green sulphur bacteria are non-motile, though one species Chloroherpeton thalassium has long, filamentous cells with gliding motility. Molecular phylogenetic analyses have placed this species as the sister taxon to all other described green sulphur bacteria.

Scanning electron micrograph of 'Chlorochromatium aggregatum', showing the green sulphur bacteria wrapped around a central (concealed) non-photosynthetic partner. Copyright American Society for Microbiology.


An interesting characteristic of many green sulphur bacteria is their propensity for forming close symbiotic relationships with other, non-photosynthetic bacteria. These associations (referred to as consortia) are so closely integrated that many were described as formal bacterial species before their composite nature was realised, and are commonly still referred to by their old 'species' names for convenience (especially as none of the bacteria involved can yet be cultured independently). In the majority of consortia, referred to as 'Chlorochromatium' and 'Pelochromatium', the non-motile green sulphur bacteria form a layer around the surface of a larger flagellated, non-photosynthetic bacterium. The motile bacterium is able to swim towards sulphide concentrations that are used for energy by the green sulphur bacteria. The oxidised sulphur or sulphate produced by the sulphur bacteria is then believed to be used by the non-photosynthetic partner for its own metabolic purposes. A slightly different type of consortium, referred to as "Chloroplana vacuolata", grows as non-motile films made up of alternating rows of the green sulphur bacteria and their colourless partners, with the one converting sulphides to sulphur or sulphates and the other converting them back again.

Short and long individuals of the non-green, not-always-sulphur bacterium Ignavibacterium album, from here.


In 2010, a group of researchers described Ignavibacterium album, currently the closest known non-photosynthetic relative of the green sulphur bacteria, from a sulphide-rich hot spring in Japan (Liu, Frigaard et al. 2012). Unlike the green sulphur bacteria, Ignavibacterium is only a facultative anaerobe, being also capable of growing in the presence of oxygen. It uses a number of electron donors including sulphide (though not elemental sulphur) and also has limited abilities to fix carbon dioxide. However, it cannot use carbon dioxide as its only carbon source in the way that the green sulphur bacteria can; as it lacks the ability to synthesise some vital amino acids, it still depends on being able to obtain those compounds from external sources. When first described, Ignavibacterium was believed to be non-motile; however, further study of its genome has identified complete versions of the genes used in flagella production. It is not unknown for motile bacteria to lose their flagella in the process of being cultured, and its seems likely that this happened to the original Ignavibacterium isolate.

A further link between Ignavibacterium and the green sulphur bacteria is provided by an organism that currently goes by the label 'Candidatus Thermochlorobacter aerophilum' (Liu, Klatt et al. 2012). As indicated by the term 'Candidatus', Thermochlorobacter has not been cultured in the laboratory. Instead, it is one of an ever-increasing number of bacterial taxa that have been identified from genetic samples extracted directly from the environment, in this case from hot springs in Yellowstone National Park. Even though these organisms have, in a sense, never been directly 'seen', we can still infer a great deal from their genomic data about what their characters are likely to be. We know that Thermochlorobacter is photosynthetic like the green sulphur bacteria, able to produce chlorosomes containing bacteriochlorophyll (probabably bacteriochlorophyll d) to obtain energy from sunlight. However, unlike the green sulphur bacteria, Thermochlorobacter lacks the ability to meet all its carbon needs by fixing carbon dioxide; like Ignavibacterium, it depends on external sources of nutrients. It is also aerobic rather than anaerobic, and lacks the ability to oxidise sulphides or sulphur. It does resemble the green sulphur bacteria in lacking the ability to produce flagella. Interestingly, however, it retains some genes that are associated in Ignavibacterium with movement towards nutrient sources; as these genes are also present in Chloroherpeton, I find myself wondering if Thermochlorobacter may be capable of gliding motility in the way that Chloroherpeton is.

REFERENCES

Garrity, G. M., & J. G. Holt. 2001. Phylum BXI. Chlorobi phy. nov. In: Boone, D. R., & R. W. Castenholz (eds) Bergey's Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 601–623. Springer.

Liu, Z., N.-U. Frigaard, K. Vogl, T. Iino, M. Ohkuma, J. Overmann & D. A. Bryant. 2012. Complete genome of Ignavibacterium album, a metabolically versatile, flagellated, facultative anaerobe from the phylum Chlorobi. Frontiers in Microbiology 3: 185. doi: 10.3389/fmicb.2012.00185.

Liu, Z., C. G. Klatt, M. Ludwig, D. B. Rusch, S. I. Jensen, M. Kühl, D. M. Ward & D. A. Bryant. 2012. ‘Candidatus Thermochlorobacter aerophilum:’ an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics. ISME Journal 6: 1869–1882. doi:10.1038/ismej.2012.24.

The Violet Demoiselle


Meet the violet demoiselle Neopomacentrus violascens (shown above in a photo by J. E. Randall). This little fish (adults get up to about 7.5 cm in length) is found in tropical waters of the western Pacific, from Japan in the north, south and east to northern Australia and Vanuatu. They usually associate in large schools around inshore reefs, and can commonly be found hanging around outcropping structures over soft bottoms such as coral or rocky outcrops, or wharf pilings (Koh et al. 1997). Violet demoiselles feed on small plant or animal plankton, such as copepods or algae.

The genus this species belongs to, Neopomacentrus, is one of the more recently recognised genera of the damselfish family Pomacentridae. It is similar to two larger genera in the family, Abudefduf and Pomacentrus, but differs from the former in having the hind margin of the preopercle (the anterior one of the bones making up the operculum or gill cover) crenulate or serrate rather than smooth. Pomacentrus has a similar preopercle, but has the suborbital region at least partially naked whereas Neopomacentrus has that region entirely scaly. Neopomacentrus violascens has a distinctive colour pattern, which is mostly a purplish brown, with bright yellow on the caudal fin and the rear of the dorsal fin.

According to Fishbase, individuals of this species form pairs when mating, and the females lay eggs that sink to the bottom and stick to the substrate. The eggs are then guarded and aerated by the males. I have come across reference to this species having been bred in captivity though I get the impression that they are not one of the most commonly kept aquarium fish. This may be because they are somewhat dull in coloration compared to related species, and they are fairly retiring in character. A recent blog post at Zoo Volunteer noted that damselfish species are rarely bred commercially due to the difficulty of providing suitable conditions. Instead, the market for species of this family is usually supplied with wild-caught individuals, commonly collected through the use of cyanide to essentially suffocate the fish until they lose conciousness. Not particularly pleasant for the fish, and arguably not that pleasant for the aquarist either as fish obtained in this method tend to have a much reduced lifespan.

REFERENCES

Koh, J. R., J. G. Myoung & Y. U. Kim. 1997. Morphological study on the fishes of the family Pomacentridae. I. A taxonomical revision of the family Pomacentridae (Pisces; Perciformes) from Korea. Korean Journal of Systematic Zoology 13 (2): 173–192.

A Place for Worms

When we think of endangered species, we tend to focus on the charismatic vertebrates, such as pandas, parrots, tigers or turtles. But endangered species may come from all walks, crawls or wriggles of life. Have you ever considered, for instance, the plight of endangered earthworms?

An unidentified species of Glossodrilus, copyright Thibaud Decaens.


Glossodrilus is a genus of earthworms found in tropical and subtropical regions of Central and South America. They are mostly fairly small as earthworms go, averaging only a few centimetres long and one or two millimetres in diameter. The largest, G. oliveirai from Brazil's Roraima State and Guyana, is about 25 centimetres long; the smallest, G. tico from Roraima and Venezuela, is less than two centimetres in length. Most species lack pigmentation, meaning that they appear greyish from the colour of their gut contents. A single species, G. freitasi from Amapá State in Brazil, is a bright violet in colour. Other diagnostic features of the genus include: eight setae per segment, arranged in regular series; a pair of (or sometimes one) calciferous glands sitting above the oesophagus in segments XI to XII; two or three pairs of lateral hearts in segments VII to IX, and two pairs of intestinal hearts in X and XI; and a pair of testes in segment XI. Glossodrilus is distinguished from a closely related earthworm genus, Glossoscolex, by the absent of a pair of muscular copulatory chambers associated with the male ducts in the latter genus (Righi 1996).

Over sixty species have been assigned to Glossodrilus; as is usual with earthworms, they are mostly distinguished by internal characters such as features of the reproductive systems. They are most diverse in upland regions, with many species inhabiting high rain forest. A few species in the northernmost or southernmost parts of the genus' range inhabit secondary grasslands. Glossodrilus species are conspicuous by their absence in the Brazilian central plateau, and only infrequently present in lowland Amazonia (Righi 1996).

And this is where the question of conservation comes in. You see, the greater number of Glossodrilus species are known only from a very restricted area (Lavelle & Lapied 2003). Part of this may be an artefact of sampling: in more recent decades, our understanding of South American earthworm diversity has been heavily shaped by one researcher, Gilberto Righi of the Universidade de São Paulo (I referred to him briefly in an earlier post on Amazonian earthworms), and we know little of areas where Righi did not collect specimens himself or from where he did not receive specimens supplied by ecological surveys. Nevertheless, sampling has probably been extensive enough to expect that the low number of shared species between different regions will hold firm at the broad scale at least. Most Glossodrilus species (and other native South American earthworms) are dependent on old-growth habitats; as land is cleared for farming, forestry and the like, exotic and invasive earthworm species take over. It would be all to easily for the little Glossodrilus to find themselves homeless, and slip into extinction without any to mark their passing.

REFERENCES

Lavelle, P., & E. Lapied. 2003. Endangered earthworms of Amazonia: an homage to Gilberto Righi. Pedobiologia 47: 419–427.

Righi, G. 1996. Colombian earthworms. Studies on Tropical Andean Ecosystems 4: 485–607.

Large Yellow Underwings


Above is an example (copyright Richard) of the large yellow underwing Noctua pronuba, the most widespread species of its genus. Noctua pronuba is a relatively large moth, with a wingspan of up to 60 mm. The forewings are fairly dull and dark in colour, but the hindwings are a bright yellow-orange (hence the vernacular name) with a black border. It can usually be found out and about in mid summer to early autumn. Its larvae are one of the types of caterpillar known as 'cutworms', which live buried in the soil during the day and emerge at night to feed. They get their vernacular name because their soil-dwelling habits mean that they tend to feed on plants from the base, often toppling small plants and seedlings like a lumberjack taking down a tree. The larvae of the large yellow underwing are not overly discerning in their food preferences; though they most often feed on grasses, they will quite happily dine on other herbaceous flowering plants such as legumes.

Larva of Noctua pronuba, copyright Nigel Richards.


The large yellow underwing is native to a wide part of the Palaearctic region, i.e. Europe and northern Asia. In 1979, it was also found introudced to Nova Scotia in North America. Since then, it has spread rapidly and can now be found over much of temperate North America, reaching British Columbia in the west and Louisiana in the south (Copley & Cannings 2005). The large yellow underwing is a strong flier and is known to undertake significant migrations in its native range. Females may also lay large numbers of eggs at a single time on the underside of leaves or on non-host plant substrates, where they can easily be carried between locales by human transportation. For the most part, a significant impact of the large yellow underwing on native or horticultural production in North America has not been recognised, though a number of authors have suggested that this species' generalist diet may lead to any such impact going unnoticed.

The Azorean Noctua atlantica, copyright Jens Jacobasch.


Historically, a large number of species have been included at one time or another in the genus Noctua, but a revision of this and closely related genera by Beck et al. (1993) cut it down on the basis of larval and male genital morphology to just two species. The only other species retained in Noctua sensu stricto by Beck et al. was N. atlantica, a species endemic to the Azores islands west of Portugal. Noctua atlantica is somewhat smaller than N. pronuba with duller hindwing coloration. It is restricted in its home range to the laurisilva, a particular subtropical forest type dominated by laurels and other evergreen, broad-leaved trees. Noctua pronuba is also found on the archipelago but inhabits are wider range of habitats. Genetic comparisons between the two species suggest that their populations diverged about five million years ago, a time frame that is not inconsistent with the origin of the Azores archipelago about four million years ago (Montiel et al. 2008). Perhaps an early population of N. pronuba became isolated on the Azores long enough to evolve into a distinct species, followed by a later re-colonisation of N. pronuba from the mainland. This would be similar to patterns seen in my home country of New Zealand, where repeated immigrations from Australia have lead to species pairs such as the endemic takahe Porphyrio hochstetteri and the more widespread pukeko P. melanotus, or the endemic (now extinct) Eyles' harrier Circus eylesi and the modern swamp harrier C. approximans.

REFERENCES

Beck, H., L. Kobes & M. Aloha. 1993. Die generische Aufgliederung von Noctua Linnaeus, 1758 (Lepldoptera, Noctuidae, Noctuinae). Atalanta 24 (1–2): 207–264.

Copley, C. R., & R. A. Cannings. 2005. Notes on the status of the Eurasian moths Noctua pronuba and Noctua comes (Lepidoptera: Noctuidae) on Vancouver Island, British Columbia. J. Entomol. Soc. Brit. Columbia 102: 83–84.

Montiel, R., V. Vieira, T. Martins, N. Simões & M. L. Oliveira 2008. The speciation of Noctua atlantica (Lepidoptera, Noctuidae) occurred in the Azores as supported by a molecular clock based on mitochondrial COI sequences. Arquipélago 25: 43–48.

ID for Heather?

The deadine for my crowdfunding drive has been extended. Thanks to your support, I am over 40% of the way towards success! But I'm still going to need everyone's help if I'm to be succesful. Please visit my page at Experiment.com and consider offering your support!


I was recently contacted by Heather Adamson who wanted to know if I could identify the animal in the above picture. She photographed it on an old post in the region of West Coolup, south of Mandurah here in Western Australia. I can tell her that it is some form of Lepidoptera larva (in other words, a caterpillar) and it looks like it may be beginning to weave itself a cocoon. Beyond that, I couldn't say. Do any of my readers have a better idea of what it is than I do?


Update: I shared this post to the Western Australian Insects group on Facebook, and Daniel Heald has suggested that Heather's photo may show the pupa of a lymantriid moth Teia athlophora. This species constructs itself a loose, cage-like cocoon from its own irritant hairs. The male, when he emerges, is a fairly standard looking brown moth, but the female is fat and flightless with only tiny stubs of wings. She will continue to live in and around her pupal cocoon, awaiting visits from courting males.

The Brown Honeyeaters

Thanks to your support, I am nearly 40% of the way towards success at my crowdfunding drive. But with only two days left on the clock, I'm going to need everyone's help if I'm to be succesful. Please visit my page at Experiment.com and consider offering your support!

Brown honeyeater Lichmera indistincta, copyright JJ Harrison.


Honeyeaters are one of the first groups of birds likely to be noticed by newcomers to Australia (after the crows and magpies, of course). Though generally not large birds, they are active, noisy and often colourful. Individuals or small groups of them will almost invariably be seen around trees in flower, seeking out nectar and squabbling over access to the best blooms.

Here in Perth, one of the more common honeyeater species is the brown honeyeater Lichmera indistincta. This is one of the smaller honeyeaters and as such might be less commonly noted by the casual observer, but it is abundant nonetheless. The brown honeyeater is one of a genus of about ten species of small, slight honeyeaters with slender decurved bills found from the Lesser Sundas of Indonesia to New Caledonia and Vanuatu (Higgins et al. 2008). Lichmera indistincta is the only species found in continental Australia. Most of the species are locally more or less abundant though some have quite restricted ranges, being found only on specific islands. A few are considered near-threatened. Lichmera species are predominantly grey-brown or greenish in colour; perhaps the most strikingly coloured is the black-necklaced honeyeater L. notabilis of the island of Wetar in the Lesser Sundas, which is yellowish-olive above and yellow below, with a striking white throat patch outlined in black.

Indonesian honeyeater Lichmera limbata, copyright Lip Kee.


Lichmera honeyeaters occupy a wide range of habitats but often prefer to be in the vicinity of water, occupying river-side woodlands and stretches of mangroves. One subspecies of the silver-eared honeyeater L. alboauricularis olivacea has a distribution that closely follows river systems in northern New Guinea. Favoured food plants of the brown honeyeater in Australia include Myrtaceae such as Eucalyptus and Melaleuca, and Proteaceae such as Banksia and Grevillea. They will also take small insects and spiders; I suspect that the proportion of nectar to insects in the diet depends on the availability of the former. Nests are open cups constructed of plant matter such as grass and pieces of bark bound together with spider web and other fibres. Small clutches of one to three eggs are brooded by the female alone, taking about two weeks to hatch, though the chicks are fed by both parents. The call of the brown honeyeater, which can be heard year-round, has been rendered as 'sweet-sweet-quarty-quarty'.

Nectar, of course, is not a hugely nutritious food source per volume (being mostly water), and a small bird like a brown honeyeater has to feed fairly constantly to keep itself going. Even though its metabolism slows down when sleeping, a brown honeyeater will still lose about half a gram of body weight overnight (Collins 1981) which is pretty impressive when you consider that the entire bire only weighs about eight grams (imagine if the average lost five kilos every night...) To make up for this loss, the bird feeds most heavily in the early morning, as well as retaining water for the last half-hour or so before going to sleep. And so it is that the honeyeater gets through the night.

REFERENCES

Collins, B. G. 1981. Nectar intake and water balance for two species of Australian honeyeater, Lichmera indistincta and Acanthorhynchus superciliosis. Physiological Zoology 54 (1): 1–13.

Higgins, P. J., L. Christidis & H. A. Ford. 2008. Family Meliphagidae (honeyeaters). In: Hoyo, J. del, A. Elliott & D. Christie (eds) Handbook of Birds of the World vol. 13. Penduline-tits to shrikes pp. 498–691. Lynx Edicions: Barcelona.