[Show abstract][Hide abstract] ABSTRACT: The evolution of sophisticated differentiations of the gastro-intestinal tract enabled herbivorous mammals to digest dietary cellulose and hemicellulose with the aid of a complex anaerobic microbiota. Distinctive symbiotic ciliates, which are unique to this habitat, are the largest representatives of this microbial community. Analyses of a total of 484 different 18S rRNA genes show that extremely complex, but related ciliate communities can occur in the rumen of cattle, sheep, goats and red deer (301 sequences). The communities in the hindgut of equids (Equus caballus, Equus quagga), and elephants (Elephas maximus, Loxodonta africanus; 162 sequences), which are clearly distinct from the ruminant ciliate biota, exhibit a much higher diversity than anticipated on the basis of their morphology. All these ciliates from the gastro-intestinal tract constitute a monophyletic group, which consists of two major taxa, i. e. Vestibuliferida and Entodiniomorphida. The ciliates from the evolutionarily older hindgut fermenters exhibit a clustering that is specific for higher taxa of their hosts, as extant species of horse and zebra on the one hand, and Africa and Indian elephant on the other hand, share related ciliates. The evolutionary younger ruminants altogether share the various entodiniomorphs and the vestibuliferids from ruminants.
European journal of protistology 01/2014; 50(2):166-173. · 1.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It is generally accepted that hydrogenosomes (hydrogen-producing organelles) evolved from a mitochondrial ancestor. However, until recently, only indirect evidence for this hypothesis was available. Here, we present the almost complete genome of the hydrogen-producing mitochondrion of the anaerobic ciliate Nyctotherus ovalis and show that, except for the notable absence of genes encoding electron transport chain components of Complexes III, IV, and V, it has a gene content similar to the mitochondrial genomes of aerobic ciliates. Analysis of the genome of the hydrogen-producing mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron transport chain that uses fumarate as electron acceptor. In addition, components of an extensive protein network for the metabolism of amino acids, defense against oxidative stress, mitochondrial protein synthesis, mitochondrial protein import and processing, and transport of metabolites across the mitochondrial membrane were identified. Genes for MPV17 and ACN9, two hypothetical proteins linked to mitochondrial disease in humans, were also found. The inferred metabolism is remarkably similar to the organellar metabolism of the phylogenetically distant anaerobic Stramenopile Blastocystis. Notably, the Blastocystis organelle and that of the related flagellate Proteromonas lacertae also lack genes encoding components of Complexes III, IV, and V. Thus, our data show that the hydrogenosomes of N. ovalis are highly specialized hydrogen-producing mitochondria.
Molecular Biology and Evolution 03/2011; 28(8):2379-91. · 14.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Many anaerobic ciliates possess hydrogenosomes, and consequently, they have the potential to host endosymbiotic methanogens.
The endosymbiotic methanogens are vertically transmitted and even the cyst stages carry methanogens. Accordingly, the analysis
of the SSU rRNA genes of ciliates and their methanogenic endosymbionts revealed that the endosymbionts are specific for their
hosts and not identical with free-living methanogens. Notably, the endosymbionts of a monophyletic group of ciliates that
thrive in either freshwater environments or intestinal tracts are substantially different. Ciliates from freshwater sediments
host methanogens belonging to the Methanomicrobiales, while ciliates thriving in the intestinal tracts of cockroaches, millipedes
and frogs host methanogens that belong to the Methanobacteriales. Comparative analysis of free-living and gut-dwelling ciliates
and their corresponding endosymbionts reveals only a limited co-evolution suggesting infrequent endosymbiont replacements.
Such an endosymbiont replacement is clearly the reason for the very distant endosymbionts of free-living and gut-dwelling
ciliates: the endosymbionts are related to the methanogens in the particular environments, in which the hosts live.
[Show abstract][Hide abstract] ABSTRACT: “Hydrogenosomes” are mitochondrion-derived, double membrane-bounded organelles that produce hydrogen and ATP. These properties
discriminate them from the likewise mitochondrion-derived “mitosomes” that produce neither hydrogen nor ATP. The only character
that is most likely shared by mitochondria, hydrogenosomes, and mitosomes is their involvement in the Fe–S metabolism.
Hydrogenosomes and mitosomes are found in a broad spectrum of rather unrelated species of unicellular, anaerobic eukaryotes,
suggesting that hydrogenosomes and mitosomes evolved repeatedly and independently in the various taxonomic groups. With the
exception of two hydrogenosomes, all these organelles lack a genome and an electron transport chain, which makes it sometimes
difficult to trace their origins back to their mitochondrial origins. However, genomic evidence, EST studies, and the analysis
of the organellar metabolism clearly reveal both a mitochondrial descent and individual differences in the properties of the
various organelles. In this paper, we describe the diversity of hydrogenosomes based predominantly on information that became
available recently. We also pay attention to the fact that certain hydrogenosomes are found in close association with endosymbiotic
[Show abstract][Hide abstract] ABSTRACT: Nearly all vertebrates host methanogens in their gastro-intestinal tracts. However, a great fraction of vertebrates emits
only traces of methane from their faeces (∼1 nmol/g faeces/h) and has no significant amounts of methane in their breath. In
contrast, many animals host some 100 times more methanogens in their gastro-intestinal tract and emit methane in their breath.
These substantial differences are not caused by different feeding habits; rather a genetic factor controls the presence of
large amounts of methanogens. The attribute “methane production” is evolutionarily stable, and the loss of this character
obeys Dollo’s law: once lost in the course of evolution, this character cannot be acquired another time.
Also invertebrates can host methanogens in their gastro-intestinal tract. In contrast to the vertebrates, only a few taxa
of arthropods emit methane: millipedes, termites, cockroaches and scarab beetles. All other arthropods in our study did not
emit methane and did not host even traces of methanogens. As in vertebrates, the diet of the animals is not crucial for the
presence of methanogens. Again, a genetic factor seems to control the presence or absence of methanogens. Methanogenesis is
also a prerequisite for the presence of intestinal anaerobic protozoa with endosymbiotic methanogens, but not for the presence
of impressive structural differentiations of the hindgut epithelium, which – in methanogenic taxa – host enormous amounts
[Show abstract][Hide abstract] ABSTRACT: Hydrogenosomes are organelles that produce molecular hydrogen and ATP. The broad phylogenetic distribution of their hosts suggests that the hydrogenosomes of these organisms evolved several times independently from the mitochondria of aerobic progenitors. Morphology and 18S rRNA phylogeny suggest that the microaerophilic amoeboflagellate Psalteriomonas lanterna, which possesses hydrogenosomes and elusive "modified mitochondria", belongs to the Heterolobosea, a taxon that consists predominantly of aerobic, mitochondriate organisms. This taxon is rather unrelated to taxa with hitherto studied hydrogenosomes.
Electron microscopy of P. lanterna flagellates reveals a large globule in the centre of the cell that is build up from stacks of some 20 individual hydrogenosomes. The individual hydrogenosomes are surrounded by a double membrane that encloses a homogeneous, dark staining matrix lacking cristae. The "modified mitochondria" are found in the cytoplasm of the cell and are surrounded by 1-2 cisterns of rough endoplasmatic reticulum, just as the mitochondria of certain related aerobic Heterolobosea. The ultrastructure of the "modified mitochondria" and hydrogenosomes is very similar, and they have the same size distribution as the hydrogenosomes that form the central stack.The phylogenetic analysis of selected EST sequences (Hsp60, Propionyl-CoA carboxylase) supports the phylogenetic position of P. lanterna close to aerobic Heterolobosea (Naegleria gruberi). Moreover, this analysis also confirms the identity of several mitochondrial or hydrogenosomal key-genes encoding proteins such as a Hsp60, a pyruvate:ferredoxin oxidoreductase, a putative ADP/ATP carrier, a mitochondrial complex I subunit (51 KDa), and a [FeFe] hydrogenase.
Comparison of the ultrastructure of the "modified mitochondria" and hydrogenosomes strongly suggests that both organelles are just two morphs of the same organelle. The EST studies suggest that the hydrogenosomes of P. lanterna are physiologically similar to the hydrogenosomes of Trichomonas vaginalis and Trimastix pyriformis. Phylogenetic analysis of the ESTs confirms the relationship of P. lanterna with its aerobic relative, the heterolobosean amoeboflagellate Naegleria gruberi, corroborating the evolution of hydrogenosomes from a common, mitochondriate ancestor.
[Show abstract][Hide abstract] ABSTRACT: There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome.
The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region) piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals.
The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial genes from other sources.
[Show abstract][Hide abstract] ABSTRACT: Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement.
We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21-29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway.
The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.
[Show abstract][Hide abstract] ABSTRACT: Fungi form avery diverse group of eukaryotes. The majority of investigated fungi contain mitochondria
and are capable of oxidative phosphorylation. On the other hand, anaerobically functioning chytridiomycete
fungi, found as symbionts in the gastrointestinal tract of many herbivorous mammals, contain hydrogenosomes.
These organelles are found in multiple classes of protozoa and catabolize glycolytic end products and produce
hydrogen and ATP by substrate-level phosphorylation. However, in contrast to the hydrogenosomes of trichomonads
and anaerobic ciliates, the hydrogenosomes of the anaerobic chytrids Neocallimastix
and Piromyces lack pyruvate dehydrogenase (PDH) and pyruvate-ferrodoxin
oxidoreductase (PFO) and instead contain pyruvate-formate lyase (PFL). The function in carbohydrate metabolism
of these hydrogenosomes of anaerobic chytridiomycete fungi and their evolutionary relation to fungal mitochondria
[Show abstract][Hide abstract] ABSTRACT: Ciliates are highly complex unicellular eukaryotes. Most of them live in aerobic environments and
possess mitochondria. However, in several orders of ciliates, anaerobic species evolved that contain “hydrogenosomes”,
organelles that produce hydrogen and ATP. These hydrogenosomes of ciliates have not been studied in the
same detail as those of trichomonads and chytrid fungi. Therefore, generalizations on the characteristics
of hydrogenosomes of ciliates are somewhat premature, especially since phylogenetic studies suggest that
hydrogenosomes have arisen independently several times in ciliates. In this chapter, the hydrogenosomes
of the anaerobic, heterotrichous ciliate Nyctotherus ovalis from the
hindgut of cockroaches will mainly be described as these are the ones that are, at the moment, the most
thoroughly studied. Thus far, this is the only hydrogenosome known to possess agenome and this genome
is clearly of mitochondrial origin. In fact, the hydrogenosome of N.ovalis
unites typical mitochondrial features such as agenome and an electron-transport chain with the most
characteristic hydrogenosomal property, the production of hydrogen. The hydrogenosomal metabolism of N.ovalis will be compared with that of two other ciliates that have been
studied in less detail, i.e. the holotrichous rumen ciliate Dasytricha,
and the free-living plagiopylid ciliate Trimyema. All studies combined
indicate that it is likely that the various types of hydrogenosomes in ciliates evolved by modifications
of aerobic mitochondria when the different ciliates adapted to anaerobic or micro aerobic environments.
Furthermore, it is clear that the hydrogenosomes of anaerobic ciliates are different from those of chytrid
fungi and from the well-studied ones in trichomonads.
[Show abstract][Hide abstract] ABSTRACT: Methanomicrococcus blatticola is an obligately anaerobic methanogen that derives the energy for growth exclusively from the reduction of methylated compounds to methane with molecular hydrogen as energy source. Competition for methanol (concentration below 10 microM) and H(2) (concentration below 500 Pa), as well as oxidative stress due to the presence of oxygen are likely to occur in the peripheral region of the cockroach hindgut, the species' normal habitat. We investigated the ecophysiological properties of M. blatticola to explain how it can successfully compete for its methanogenic substrates. The organism showed affinities for methanol (K(m)=5 microM; threshold<1 microM) and hydrogen (K(m)=200 Pa; threshold <0.7 Pa) that are superior to other methylotrophic methanogens (Methanosphaera stadtmanae, Methanosarcina barkeri) investigated here. Thermodynamic considerations indicated that 'methanol respiration', i.e. the use of methanol as the terminal electron acceptor, represents an attractive mode of energy generation, especially at low hydrogen concentrations. Methanomicrococcus blatticola exploits the opportunities by specific growth rates (>0.2 h(-1)) and specific growth yields (up to 7 g of dry cells per mole of methane formed) that are particularly high within the realm of mesophilic methanogens. Upon oxygen exposure, part of the metabolic activity may be diverted into oxygen removal, thus establishing appropriate anaerobic conditions for survival and growth.
[Show abstract][Hide abstract] ABSTRACT: The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I.
The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome.
The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering.
[Show abstract][Hide abstract] ABSTRACT: The eukaryotic biodiversity in historical air-dried samples of Dutch agricultural soil has been assessed by random sequencing of an 18S rRNA gene library and by denaturing gradient gel electrophoresis. Representatives of nearly all taxa of eukaryotic soil microbes could be identified, demonstrating that it is possible to study eukaryotic microbiota in samples from soil archives that have been stored for more than 30 years at room temperature. In a pilot study, 41 sequences were retrieved that could be assigned to fungi and a variety of aerobic and anaerobic protists such as cercozoans, ciliates, xanthophytes (stramenopiles), heteroloboseans, and amoebozoans. A PCR-denaturing gradient gel electrophoresis analysis of samples collected between 1950 and 1975 revealed significant changes in the composition of the eukaryotic microbiota.
[Show abstract][Hide abstract] ABSTRACT: A continuous wave, single frequency and continuously tunable optical parametric oscillator is used in combination with photoacoustic spectroscopy to detect trace emissions of CO2 from insects under atmospheric conditions. The optical parametric oscillator (OPO) contains a periodically poled lithium niobate crystal and is tunable over the 3.9 to 4.8 mum infrared wavelength region. With the strong rotational-vibrational absorption band of CO2 at 4.23 mum, it is possible to detect CO2 down to 7 parts per billion volume using 20 mW of the OPO beam. This detection sensitivity was achieved by adding 4% of SF6 gas to the atmospheric gas mixture to overcome the slow vibrational relaxation of the excited CO2 levels. The usefulness of this system is demonstrated by real-time measuring of the fluctuations of the CO2 concentration in the breath of a single ant (Lasius niger) and individual fruit flies (Drosophila melanogaster).
Applied Physics B 02/2006; 82:665-669. · 1.78 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Hydrogenosomes are not the same. They evolved several times — independently — from mitochondria or the common ancestor of
hydrogenosomes and mitochondria. This process, in general, involved the loss of the organellar genome together with the mitochondrial
electron transport chain, and metabolic adaptations to anoxic environments such as the use of protons as terminal electron
acceptors. Substantial differences in the physiological capacities of the various hydrogenosomes reflect their independent
evolution through evolutionary tinkering. Notably, even the common denominator of these organelles, i.e., the production of
hydrogen, can become marginal in certain hydrogenosomes.
The hydrogenosomal metabolism is crucial for the establishment of symbiotic associations, and sometimes differences in the
host’s metabolism seem to be able to provide the clues for an understanding of the presence or absence of pears to be insufficient
to explain the observations. Obviously, intrinsic properties of the various hosts and their symbionts play an important role,
which are, at the moment, clearly not even beyond the level of a preliminary phenomenological description. Intensive efforts
are required to analyse the elusive molecular basis of symbiotic associations. Many fascinating insights into the secrets
of symbiotic associations await their discovery.
Progress in molecular and subcellular biology 02/2006; 41:117-42.
[Show abstract][Hide abstract] ABSTRACT: The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium).
A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates.
Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.
[Show abstract][Hide abstract] ABSTRACT: Biogenic methane contributes substantially to the atmospheric methane concentration and thus to global warming. This trace gas is predominantly produced by strictly anaerobic methanogenic archaea, which thrive in the most divergent ecological niches, e. g. paddy fields, sediments, landfills, and the digestive tract of various animals. Methanogenic archaea also live as endosymbionts in the cytoplasm of anaerobic protozoa. In marine sediments these endosymbionts can contribute up to 90% to the overall rate of methanogenesis, whereas their role of in freshwater sediments is largely unknown. Here we describe the results of a one year's survey of the methanogenesis by endosymbiotic methanogens in four different Dutch freshwater sediments. The abundance of anaerobic protozoa, in particular ciliates, the methane production rates by the ecosystem and by the protists, and a number of abiotic parameters were measured. A novel method (heatshock for 5 min) for estimating the contribution by endosymbiotic methanogens was established. Our results reveal large fluctuations of ciliate abundance throughout the year, but on average, only minor contributions by methanogenic endosymbionts to the total methanogenesis in these environments