Field of Science

What We Have Here is a Failure to Communicate

To those without much of a background in taxonomy, the various rules governing the naming of organisms can seen frustratingly byzantine and laborious. "Surely," they think to themselves as they despairingly attempt to come to grips with concepts of holotypes and lectotypes, synonyms and homonyms, "there must be an easier way of doing this". Nevertheless, the easiest way to develop an appreciation for just how valuable it is to have a set of rules governing nomenclature is to attempt to deal with anything dating back to the days before such rules were established. Settle back, readers, while I tell you a tale. Pour yourself a drink. You're going to hate this.

Collonista glareola, a species that just might be related to the subject of this post, copyright Huang, Fu & Poppe.

These days, it is generally accepted that before a new name can enter general use, it should be clearly established in some form of formal, widely-accessible publication just to what it is that the name is supposed to refer. Back in the day, however, this was not always the case. A century or two ago, the communities of researchers working on a particular group of organisms were often small, and it was not uncommon for names to effectively spread through personal correspondence or word of mouth alone. One naturalist might refer to a new genus he had come to recognise in a letter to another, and the latter naturalist may then assign his own species to that genus without the first naturalist ever publishing a formal description. At the time, this might not be seen as much of an issue: after all, if there was ever any question as to the first naturalist's original intent, surely it could be clarified by simply writing to him personally?

The name Leptothyra seems to have been established in this kind of way in the mid-1800s by the American naturalist James Graham Cooper for a genus of small marine gastropods (belonging to the vetigastropods, related to the top shells and cat's-eyes) found on the coast of California. In 1871, W. H. Dall attributed the name to an unpublished manuscript of Cooper's and cited the type species as Linnaeus' Turbo sanguineus, a Mediterranean species to which Cooper had also attributed specimens from the Pacific. As it happens, Turbo sanguineus was already the type species for an earlier genus name, Homalopoma, so Dall's 'Leptothyra' would be considered invalid and give precedence to Homalopoma. However, in 1869 the name Leptothyra had been used by W. H. Pease for L. costata, a species from Hawaii, without direct reference to any other species (thus making L. costata the effective type species of Leptothyra). Subsequent authors often considered 'Leptothyra Pease' to be a separate genus from Homalopoma/'Leptothyra Dall'. At least one author who did not, Henry A. Pilsbry (1888), nevertheless used the name Leptothyra under the mistaken belief that the name Homalopoma was preoccupied. Over time, numerous species both living and fossil from around the Pacific were assigned to Leptothyra in one way or another.

It was not until over a century later that Coan (1986) pointed out that the name Leptothyra had appeared in print even earlier than Pease's usage. Cooper himself had used the name in a list of Californian molluscs in 1867. Even though Cooper's list lacked any descriptive details, this counts as enough to validate the name because he included species for which descriptions had already been published under other genera. One of these was Turbo sanguineus, which Coan officially designated as type species and fixed Leptothyra's status as an invalid later name for Homalopoma.

Which leaves open the question of what one should call the genus formerly known as 'Leptothyra Pease'. It doesn't help matters that Pease's 'Leptothyra costata' has apparently never been illustrated and its identity has been open to question. Iredale (1918) proposed the name Collonista for use with species previously included in Leptothyra, stating that the latter "proves to have been first published by Pease in connexion with a juvenile shell of a different genus", but gave no further elaboration or explanation how he reached that conclusion. The online resource WoRMS lists L. costata as a junior synonym of the widespread Pacific species Collonista verruca, but I have been unable to find where that synonymy was published. Nevertheless, any sort of replacement name for 'Leptothyra Pease' seems like it would be misguided at best. It is unlikely that L. costata represents any genus otherwise unknown and, even without any explicit statement to the effect, it is quite possible that Pease only intended to assign his species to Cooper's manuscript genus rather than establish a new genus of his own. Any concept of a genus Leptothyra is best left to sink into the annals of history.


Coan, E. 1986. Some additional taxonomic unites that first appear in publications by J. G. Cooper. Nautilus 100 (1): 30–32.

Cooper, J. G. 1867. Geographical catalogue of the Mollusca found west of the Rocky Mountains, between latitudes 33° and 49° north. Geological Survey of California: San Francisco.

Dall, W. H. 1871. Descriptions of sixty new forms of mollusks from the west coast of North America and the North Pacific Ocean, with notes on others already described. American Journal of Conchology 7 (2): 93–160, pls 13–16.

Iredale, T. 1918. Molluscan nomenclatural problems and solutions.—No. 1. Proceedings of the Malacological Society of London 13 (1–2): 28–40.

Pease, W. H. 1869. Descriptions of new species of marine Gasteropodae inhabiting Polynesia. American Journal of Conchology 5 (2): 64–79.

Philonthus: Too Many Staphylinids

Philonthus marginatus, copyright James K. Lindsey.

Working with staphylinids, it has to be said, can be horrible. They are treated as one of the most diverse of the beetle families—perhaps the most diverse of all—but compared to other diverse families they attract relatively little study. The majority of staphylinids are usually either very small or soft-bodied, not uncommonly both together, making them difficult to prepare and maintain as dry specimens. For the soft-bodied species, with their reduced elytra, many of the easily visible features that can be so useful for other beetle groups are obscure or unavailable. They also tend to be drab in coloration, without much in the way of striking patterning. As a result, it is often impossible to identify staphylinid species without examining minute features of the appendages or the genitalia. Something to keep in mind as you read the following.

Species of the genus Philonthus are relatively large as staphylinids go, often about half a centimetre in length, but they are certainly not free of the problems affecting other members of the family taxonomy-wise. The genus is massively diverse—over 1200 species have been described from around the world. Attempts have been made to break them down into more manageable chunks, such as through the recognition of subgenera, but these have mostly failed to gain much traction. Most recent authors have only recognised informal species groups within the greater mass.

Philonthus carbonarius, copyright James K. Lindsey.

In general, species of Philonthus are smooth, without excessive hairs, and have labial palps with the last segment fusiform and about as wide as the penultimate segment (Tottenham 1955; Stan 2012). Males have the aedeagus (the intromittent organ of the genitalia) rotated in the abdomen so its paramere (off-branch) is located on the left side rather than ventrally as in other genera (Tottenham 1955). Some species may have a metallic sheen to their coloration; others are a plainer black or reddish. Species may also differ in the number and arrangement of setae on the pronotum.

Where their lifestyles are known, most Philonthus are associated with decomposing organic matter such as animal dung, compost or leaf litter. Some are predators of other insects and insect larvae found in such habitats (such as fly larvae); these species have highly developed senses to locate decaying matter, and are strong fliers to disperse to suitable habitats (Majka et al. 2009). Some species of Philonthus may act as predators of other pest insects, helping to keep their numbers down.


Majka, C. G., J.-P. Michaud, G. Moreau & A. Smetana. 2009. Philonthus hepaticus (Coleoptera, Staphylinidae) in eastern Canada: are distribution gaps distinctive features or collecting artifacts? ZooKeys 22: 347–354.

Stan, M. 2012. On the species of Philonthus Stephens (Coleoptera: Staphylinidae: Staphylininae: Staphylinini: Philonthina) in the collections of Romanian natural history museums. Travaux du Muséum National d'Histoire Naturelle "Grigore Antipa" 55 (2): 233–276.

Tottenham, C. E. 1955. Studies in the genus Philonthus Stephens (Coleoptera: Staphylinidae). Parts II, III, and IV. Transactions of the Royal Entomology Society of London 106 (3): 153–195.

A Question of Taste

The Hawaiian Islands have provided us with a number of impressive examples of species radiations. Some of these, such as the Hawaiian honeycreepers, are well known to the general public. Others, such as the subject of today's post, may not be so famous but are no less noteworthy nonetheless.

Individual of a Laupala species, copyright K. Shaw.

Laupala is a genus of crickets distributed between all of the main islands of the Hawaiian chain. For a long time, they were all believed to belong to a single species referred to as Paratrigonidium pacificum. However, in the late 1960s, two entomologists, Richard Alexander and David Otte, started taking recordings of the songs of Hawaiian crickets. They began to realise that individuals of 'Paratrigonidium pacificum' from different localities had noticeably distinct songs. Most of these songs consisted of a fairly basic series of regular pulses of sound, but the frequency of the pulses could vary from only one every three seconds to four every second. Some of the song types were extremely localised; Otte (1994) referred to an occasion when he lost his car keys while out collecting at night, and was able to relocate the area he had been in and find his keys by following which crickets were singing. There might be one song pattern to be heard on the windward side of a ridge and an entirely different pattern on the leeward side (admittedly, in the precipitous landscape of many parts of the Hawaiian Islands, a 'ridge' an amount to a pretty serious geological barrier) Eventually, Otte (1994) would recognise the earlier 'Paratrigonidium pacificum' as including over thirty species of Laupala, plus a couple of species distinctive enough to be placed in a related genus, Prolaupala. Some of these species can be distinguished by their external appearance, albeit by relatively minor variations in coloration and patterning that would not be easily picked up, or by features of the male genitalia. Many cannot and can only be distinguished by the songs of the males.

All indications are that the Laupala have undergone rapid evolution to reach their current diversity. The oldest of the islands that Laupala species have been found on to date, Kauai, is about five millions years old. The big island of Hawai'i is less than a million years in age. Nor, of course, is there any reason to assume that the crickets have stopped diversifying. Laupala cerasina, a species found over a large part of the island of Hawai'i, is highly variable in both song pattern and morphological features; indeed, variation between populations of L. cerasina is such that they could easily be regarded as separate species were it not for the failure (to date) to identify clear separation between the variants. A comparison between phylogeny of the genus and island age suggests that Laupala species have been diverging at a rate of up to more than four speciation events per million years (Mendelson & Shaw 2005). This is one of the fastest recorded rates of speciation in the animal kingdom; only African cichlids have been calculated to be diversifying faster. It is perhaps not surprising that both of these cases of rapid speciation appear to be driven by features related to sexual selection; it has been suggested that the power of sexual selection is such that what amount to questions of taste can cause wholesale change in populations within a matter of generations. Patterns of variation observed within different species of Laupala are also consistent with the predictions of sexual selection: on the island of Oahu, the species L. pacifica has a song that is noticeably faster in localities where it co-exists with the slower-singing L. spissa than in localities where it is the only species.

Results of phylogenetic analyses from Shaw (2002), showing disagreements between nuclear and mitochondrial genetic analyses.

The Laupala radiation also resembles that of the cichlids in that it gets more complicated the closer one looks. In his original description of the radiation, Otte (1994) recognised three species groups, separated on the basis of morphological features. One of these, the L. kauaiensis group, contains those species found on the island on Kauai. As befits Kauai's position as the oldest and most isolated of the islands involved, phylogenetic studies agree that this species group is well separated from the other two. The other two, more diverse, groups, the L. cerasina and L. pacifica groups, are each dispersed over the islands of Oahu, Maui and Hawai'i (the L. cerasina group also includes two species on the island of Molokai). Analyses of nuclear genetic data support these species groups, implying multiple dispersals between islands. The phylogeny presented by Mendelson & Shaw (2005) on the basis of AFLP (amplified fragment length polymorphism) data is consistent with divergence of the two groups on Oahu followed by sequential dispersal of each of the two groups down the line of newly emerging islands; an earlier phylogeny presented by Shaw (2002) on the basis of nuclear sequence analysis is perhaps a bit less tidy but still fits the same overall framework. However, an analysis of mitochondrial genetic data that was also presented by Shaw (2002) presents a quite different picture. With the exception of the Kauai group, Otte's species groups were not supported by the mitochondrial data. Instead, two species from a single island that might be placed in separate groups by the morphological and nuclear data would be placed close together by the mitochondrial data.

How can this discrepancy between the data sources be explained? The most likely explanation is that the nuclear and mitochondrial data reflect different genetic histories. Because mitochondria are inherited only in the maternal line, interbreeding between individuals of different species can result in progeny containing nuclear and mitochondrial genes with entirely distinct heritages. The implication is that the boundaries between Laupala species have not been impervious, that there has been a certain degree of hybridisation in the past. Again, there are reasons for finding this credible. Studies of mating behaviour in Laupala have found that, as a species isolating device, song patterns are only effective at a long range. Females will only actively seek out males producing the right song patterns, but they will not refuse males singing differently whom they happen to encounter on the way. Song patterns are not the only reasons a female may have for refusal; for instance, Mullen et al. (2007) identified a distinct separation between species by cuticular chemistry, implying that individuals of different species smell or taste as well as smell different. Nevertheless, species of this genus diverged recently enough that it is quite credible that they could remain interfertile when the occasion arose.


Mendelson, T. C., & K. L. Shaw. 2005. Rapid speciation in an arthropod. Nature 433: 375–376.

Mullen, S. P., T. C. Mendelson, C. Schal & K. L. Shaw. 2007. Rapid evolution of cuticular hydrocarbons in a species radiation of acoustically diverse Hawaiian crickets (Gryllidae: Trigonidiinae: Laupala). Evolution 61 (1): 223–231.

Otte, D. 1994. The Crickets of Hawaii: Origin, Systematics and Evolution. Orthopterists' Society, Academy of Natural Sciences of Philadelphia.

Shaw, K. L. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: what mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proceedings of the National Academy of Sciences of the USA 99 (25): 16122–16127.

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.


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.


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.