Molecular phylogeny of euthyneura (mollusca: gastropoda)

A new phylogenetic hypothesis for Euthyneura is proposed based on the analysis of primary sequence data (mitochondrial cox1, trnV, rrnL, trnL(cun), trnA, trnP, nad6, and nad5 genes) and the phylogenetic utility of two rare genomic changes (the relative position of the mitochondrial trnP gene, and an insertion/deletion event in a conserved region of the mitochondrial Cox1 protein) is addressed. Both sources of phylogenetic information clearly rejected the monophyly of pulmonates, a group of gastropods well supported so far by morphological evidence. The marine basommatophoran pulmonate Siphonaria was placed within opisthobranchs and shared with them the insertion of a Glycine in the Cox 1 protein. The marine systellommatophoran pulmonate Onchidella was recovered at the base of the opisthobranch + Siphonaria clade. Opisthobranchs, Siphonaria, and Onchidella shared the relative position of the mitochondrial trnP gene between the mitochondrial trnA and nad6 genes. The land snails and slugs (stylommatophoran pulmonates) were recovered as an early split in the phylogeny of advanced gastropods. The monophyly of the Euthyneura (Opisthobranchia + Pulmonata) was rejected by the inclusion of the heterostrophan Pyramidella.     

HELICOIDAL ARCHITECTURE IN THE PERIOSTRACUM OF A TERRESTRIAL PROSOBRANCH PTEROCYCLUS LATILABRUM SMITH

In the land prosobranch gastropod Pterocyclus latilabrum Smiththe periostracum is composed of a scleroprotein with polar characterresembling compositionally more the periostraca of many marineprosobranchs and some terrestrial or freshwater pulmonates thanthose of certain other land-living species of pulmonate or mostof the freshwater prosobranchs. The periostracum is a lamellarstructure with a distinctive ultrastructural organization showingevidence for a preferred orientation of microfibrils in helicoidallystacked layers. (Received 20 August 1984;     

An investigation of the "Ancyloplanorbidae" (Gastropoda, Pulmonata, Hygrophila): preliminary evidence from DNA sequence data

The Planorbidae is the largest family of freshwater pulmonate snails, yet an understanding of their intrafamily phylogenetic relationships is lacking and existing inferences are tentative. Moreover, it has been suggested that the Ancylidae, limpet-like freshwater pulmonates, should be merged with Planorbidae according to analysis of internal organ morphology. The present study explicitly tests this hypothesis by phylogenetic inference from partial DNA sequences of three molecular markers, nuclear ribosomal small subunit 18S and the mitochondrial cytochrome oxidase, and large subunit 16S. A molecular phylogeny was inferred based upon 22 taxa representing 12 ancylid and planorbid genera; additional taxa were included from the authors' database and from available sequences from GenBank, to further explore this basic data set. Taxa from Acroloxidae, Lymnaeidae, and Physidae were used as outgroups. Ancylidae and Planorbidae were found to be paraphyletic, with Planorbidae including some members of Ancylidae. "Ancyloplanorbidae" was also found to be paraphyletic because Acroloxus (Acroloxidae) surprisingly was included. Burnupia was found to be ancestral to "Ancyloplanorbidae" (including Acroloxus). The following clades of Planorbidae were supported: Bulininae and Planorbinae, Biomphalarini (including Helisoma and Planorbarius), and Planorbini and Segmentini.     

Native and introduced land snail species as ecological indicators in different land use types in Java

We investigated the effects of different land use types and environmental parameters on the number and abundance of native and introduced land snail species in East Java. 2919 specimens were sampled and assigned to 55 species of which 8 are introduced. Whereas species richness was highest in primary forest, the highest number of introduced species was found in agroforest. The snail assemblages in different habitat types differ much clearer in composition than in total species richness. Plantations and agroforest are dominated by introduced pulmonates with regard to number of individuals, while primary forest is dominated by native prosobranchs. The habitat requirements of the introduced pulmonates differ from those of the native species. In the study area, the abundance of native as well as introduced pulmonate species increased with increasing human impact. However, the abundance of introduced pulmonate species decreased with increasing density of the canopy cover, whereas the abundance of native pulmonate species increased with increasing canopy cover. The abundance of native prosobranch land snails also tends to increase with increasing canopy cover and with the availability of deadwood, but decreased with increasing human impact. Improving the canopy cover and retaining deadwood in plantations and agroforests might help to control the populations of introduced species or even prevent their establishment in these habitats. Land snails are good indicators for the long-term stability of natural habitats, because several species are restricted to undisturbed natural habitats and because of their low dispersal abilities. However, complete inventories of land snail species are costly. Therefore we propose two indices that can be scored with much less effort, namely the percentage of prosobranch individuals and the percentage of individuals of introduced species. Both indices are significantly correlated with the number of native species. Dense plantations and agroforests bordering primary forests may protect the latter from introduced species and help to conserve the native fauna by reducing desiccation and buffering the human impact on the primary forests.     

Musculature of the penial complex: A new criterion in unravelling the phylogeny of Hygrophila (Gastropoda: Pulmonata)

The taxonomy of freshwater pulmonates (Hygrophila) has been in a fluid state warranting the search for new morphological criteria that may show congruence with molecular phylogenetic data. We examined the muscle arrangement in the penial complex (penis and penis sheath) of most major groups of freshwater pulmonates to explore to which extent the copulatory musculature can serve as a source of phylogenetic information for Hygrophila. The penises of Acroloxus lacustris (Acroloxidae), Radix auricularia (Lymnaeidae), and Physella acuta (Physidae) posses inner and outer layers of circular muscles and an intermediate layer of longitudinal muscles. The inner and outer muscle layers in the penis of Biomphalaria glabrata consist of circular muscles, but this species has two intermediate longitudinal layers separated by a lacunar space, which is crossed by radial and transverse fibers. The muscular wall of the penis of Planorbella duryi is composed of transverse and longitudinal fibers, with circular muscles as the outer layer. In Planorbidae, the penial musculature consists of inner and outer layers of longitudinal muscles and an intermediate layer of radial muscles. The penis sheath shows more variation in muscle patterns: its muscular wall has two layers in A. lacustris, P. acuta, and P. duryi, three layers in R. auricularia and Planorbinae and four layers in B. glabrata. To trace the evolution of the penial musculature, we mapped the muscle characters on a molecular phylogeny constructed from the concatenated 18S and mtCOI data set. The most convincing synapomorphies were found for Planorbinae (inner and outer penis layers of longitudinal muscles, three-layered wall of the penis sheath). A larger clade coinciding with Planorbidae is defined by the presence of radial muscles and two longitudinal layers in the penis. The comparative analysis of the penial musculature appears to be a promising tool in unraveling the phylogeny of Hygrophila.     

Osmotic Balance in a Marine Pulmonate,Amphibola crenata

The pulmonate mud‐snail Amphibola crenata is an osmoconformer in 25%‐125% sea water, its haemolymph being slightly hyperosmotic and hyperionic to the medium. It maintains its haemolymph markedly hyperosmotic in media below 25% sea water and in freshwater, in which it survives for a week or longer. On exposure to dilute or concentrated media, water which enters or leaves the tissues preferentially enters or leaves the cells. Regulation of cell volume towards initial values is accomplished within 5 days. Measurements of changes in cell volume, and of distribution of tissue water between the intracellular and extracellular compartments, in snails moved from 100% sea water into dilute or concentrated media, and in snails moved back to 100% sea water, indicate that mechanisms of cell volume regulation are minimal in ca 60–65% sea water. Changes in the concentration of tissue free amino acids are in accord with current theories of mechanisms of isosmotic intracellular regulation. The results are discussed in the light of the taxonomic, evolutionary and ecological status of Amphibola as a shore‐living, primitive, marine representative of a predominantly terrestrial and freshwater group of gastropod molluscs.     

Habitat and phylogeny influence salinity discrimination in crocodilians: implications for osmoregulatory physiology and historical biogeography

Crocodylids are better adapted than alligatorids, through a suite of morphological specializations, for life in hyperosmotic environments. The presence of such specializations even in freshwater crocodylids has been interpreted as evidence for a marine phase in crocodylid evolution, consistent with the trans-osceanic migration hypothesis of crocodilian biogeography. The ability to discriminate fresh water from hyperosmotic sea water, and to avoid drinking the latter, is known to be an important osmoregulatory mechanism for estuarine crocodylids. This study was undertaken to determine whether the ability to discriminate between hyper- and hypo-osmotic salinities is determined by habitat, as it is in other normally freshwater reptiles, or whether, like morphological adaptations associated with estuarine life, it has a phylogenetic basis. Two species of freshwater alligatorid were found to drink fresh water and hyperosmotic sea water indiscriminately, while an estuarine population of a normally freshwater alligatorid species drank only fresh water. This indicated that salinity discrimination is determined at least in part by habitat. However, all three crocodylid species tested drank fresh water but not hyperosmotic sea water, suggesting that, in crocodilians, the ability to distinguish between fresh water and sea water is influenced by phylogeny as well as by habitat. The implications of this result are discussed in the context of two alternate hypotheses for the historical biogeography of the Crocodilia.     

Differences in dispersal- and colonization-related traits between taxa from the freshwater and the terrestrial realm

The aquatic and terrestrial realms differ in many physical properties that not only require specific physiological adaptations but also cause differences in dispersal options. We thus expect that life-history traits related to dispersal and colonization are under selection pressure because freshwater habitats are more isolated and thus more difficult to reach. We compared traits from European databases of three taxonomic groups along the passive–active dispersal gradient: plants (Plantes), snails (Mollusca: Gastropoda: Prosobranchia et Pulmonata) and hoverflies (Diptera: Syrphidae), all of which have both terrestrial and freshwater species (plants and snails) or early life stages (hoverflies). Aquatic taxa seem to be more successful long-distance dispersers than are terrestrial taxa. Our analysis also revealed lower numbers of seeds or eggs produced in the aquatic habitats. However, aquatic taxa often allocate resources to offspring guarding (vegetative propagules in plants, egg capsules in snails) and breeding-site selection (syrphids). Colonization of the aquatic realm is reinforced by increases in life span (plants), clonal spread (plants), shorter generation times (snails), selfing ability (marginal effect in pulmonate snails) or paedogenesis (two incidences in hoverflies, needs further studies). Probably, the variety of strategies reflects the different evolutionary backgrounds that elicit different combinations of trade-offs, but all traits also might increase invasibility of species.     

Larger genomes for molluskan land pioneers.

The terrestrial pulmonate mollusks were found to have the significantly larger genomes than the aquatic pulmonates. Being shown in the independent phylogenetic branch, this phenomenon suggests that the previously observed genome enlargement in the vertebrate land pioneers (amphibians and lungfishes) was not casual. As in the vertebrates, the larger molluskan genomes are also more GC-rich.     

DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE‐DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE)

Freshwater habitats make up only ～0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time‐calibrated phylogeny and a state‐dependent speciation–extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state‐dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage‐through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase.     

Small fish, big fish, red fish, blue fish: size-biased extinction risk of the world's freshwater and marine fishes

Aim  In light of the current biodiversity crisis, there is a need to identify and protect species at greatest risk of extinction. Ecological theory and global-scale analyses of bird and mammal faunas suggest that small-bodied species are less vulnerable to extinction, yet this hypothesis remains untested for the largest group of vertebrates, fish. Here, we compare body-size distributions of freshwater and marine fishes under different levels of global extinction risk (i.e. listed as vulnerable, endangered or critically endangered according to the IUCN Red List of Threatened Species ) from different major sources of threat (habitat loss/degradation, human harvesting, invasive species and pollution).
Location  Global, freshwater and marine.
Methods  We collated maximum body length data for 22,800 freshwater and marine fishes and compared body-size frequency distributions after controlling for phylogeny.
Results  We found that large-bodied marine fishes are under greater threat of global extinction, whereas both small- and large-bodied freshwater species are more likely to be at risk. Our results support the notion that commercial fishing activities disproportionately threaten large-bodied marine and freshwater species, whereas habitat degradation and loss threaten smaller-bodied marine fishes.
Main conclusions  Our study provides compelling evidence that global fish extinction risk does not universally scale with body size. Given the central role of body size for trophic position and the functioning of food webs, human activities may have strikingly different effects on community organization and food web structure in freshwater and marine systems.     

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): new insights from increased taxon sampling

Phylogenetic relationships among higher clades of pulmonate gastropods are reconstructed based on a data set including one nuclear marker (complete ribosomal 18S) and two mitochondrial markers (partial ribosomal 16S and Cytochrome oxidase I) for a total of 96 species. Sequences for 66 of these species are new to science, with a special emphasis on sampling the Ellobiidae, Onchidiidae, and Veronicellidae. Important results include the monophyly of Systellommatophora (Onchidiidae and Veronicellidae) as well as the monophyly of Ellobiidae (including Trimusculus, Otina, and Smeagol). Relationships within Ellobiidae, Onchidiidae, and Veronicellidae are evaluated here for the first time using molecular data. Present results are compared with those from the recent literature, and the current knowledge of phylogenetic relationships among pulmonate gastropods is reviewed: despite many efforts, deep nodes are still uncertain. Identification uncertainties about early fossils of pulmonates are reviewed. Impacts of those phylogenetic and fossil record uncertainties on our understanding of the macro-evolutionary history of pulmonates, especially transitions between aquatic and terrestrial habitats, are discussed.     

Copper in Helix pomatia (Gastropoda) is regulated by one single cell type: differently responsive metal pools in rhogocytes

Like all other animal species, terrestrial pulmonate snails require Cu as an essential trace element. On the other hand, elevated amounts of Cu can exert toxic effects on snails. The homeostatic regulation of Cu must therefore be a pivotal goal of terrestrial pulmonates to survive. Upon administration of Cu, snails accumulate the metal nearly equally in most of their organs. Quantitative studies in connection with HPLC and electrospray ionization mass spectrometry reveal that a certain fraction of Cu in snails is bound to a Cu-metallothionein (Cu-MT) isoform that occurs in most organs at constant concentrations, irrespective of whether the animals had been exposed to physiological or elevated amounts of Cu. In situ hybridization demonstrates that at the cellular level, the Cu-binding MT isoform is exclusively expressed in the so-called pore cells (or rhogocytes), which can be found in all major snail organs. The number of pore cells with Cu-MT mRNA reaction products remains unaffected by Cu exposure. Rhogocytes also are major storage sites of Cu in a granular form, the metal quickly entering the snail tissues upon elevated exposure. The number of rhogocytes with granular Cu precipitations strongly increases upon Cu administration via food. Thus, whereas Cu-MT in the rhogocytes represents a stable pool of Cu that apparently serves physiological tasks, the granular Cu precipitations form a second, quickly inducible, and more easily available pool of the metal that serves Cu regulation by responding to superphysiological metal exposure.     

Global Ecological Pattern of Ammonia-Oxidizing Archaea

Background

The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent.

Methodology and Results

We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats.

Conclusion and Significance

Based on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.     

The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.     

Relative vulnerability of six freshwater gastropods to the leech Nephelopsis obscura (Verrill)

SUMMARY. 1. The vulnerability of six species of freshwater snails to the leech Nephelopsis obscura was determined in laboratory predation experiments.
2. Nephelopsis was unable to prey on prosobranch snails with an operculum, but did consume certain pulmonate species though predation rates were low, ranging from one to two snails per leech per night at 20°C. Apparently, Nephelopsis does not actively select prey, but merely consumes those species most easily handled.
3. Among pulmonates, leeches captured species in the following order: Physa gyrina (Say), Helisoma anceps (Menke). Lymnaea emarginata (Say) and Helisoma trivolvis (Say). Susceptibihty of size classes varied among snail species.
4. Neither environmental structure, such as cobble or macrophytes, nor gastropod escape behaviors, such as clamping to substrates or vertical migration away from bottom-feeding leeches, lowered capture rates by Nephelopsis.
5. In 2 years sampling, only one of seven lakes, however, had appreciable abundances of Nephelopsis. It is therefore suggested that the rarity, low feeding rates, and lack of strong gastropod preference limit the effect of Nephelopsis on field gastropod distributions.     

Can export of organic matter from estuaries support zooplankton in nearshore,marine plumes?

Marine and terrestrial ecosystems are connected via transfers of nutrients and organic matter in river discharges. In coastal seas, such freshwater outflows create prominent turbidity plumes. These plumes are areas of high biological activity in the pelagos, of which zooplankton is a key element. Conceptually, the increased biomass of zooplankton consumers in plumes can be supported by two alternative trophic pathways—consumption of fresh marine phytoplankton production stimulated by riverine nutrients, or direct trophic subsidies through the uptake of terrestrial and estuarine organic matter flushed to sea. The relative importance of these two pathways has not been established previously. Isotopic tracing (carbon and nitrogen) was used to measure the extent of incorporation of marine versus terrestrial matter into mesozooplankton consumers in the plumes off a small estuary in eastern Australia. Replicate zooplankton samples were taken during baseflow conditions with minimal freshwater influence to the sea, and during pulsed discharge events that generated turbidity plumes in coastal waters. Food sources utilized by zooplankton differed among locations and with the strength of freshwater flow. Terrestrial and estuarine carbon only made a sizeable contribution (47%) to the carbon demands of zooplankton in the lower estuary during pulsed freshwater flows. By contrast, in plumes that developed in nearshore marine waters, phytoplankton supplied up to 90% of the dietary carbon of zooplankton feeding in the plumes. Overall, it was “fresh” carbon, fixed by marine phytoplankton, the growth of which became stimulated by fluvial nutrient exports, that dominated energy flows in plume regions. The trophic role of terrestrial and estuarine organic exports was comparatively minor. The trophic dynamics of plankton in small coastal plumes is closely linked to variations in freshwater flow, but this coupling operates mainly through the enhancement of in-situ phytoplankton production rather than cross-boundary transfers of organic matter to marine food webs in the pelagos.     

Marine-freshwater colonizations of haptophytes inferred from phylogeny of environmental 18S rDNA sequences

The Haptophyta is a common algal group in many marine environments, but only a few species have been observed in freshwaters, with DNA sequences available from just a single species, Crysochromulina parva Lackey, 1939. Here we investigate the haptophyte diversity in a high mountain lake, Lake Finsevatn, Norway, targeting the variable V4 region of the 18S rDNA gene with PCR and 454 pyrosequencing. In addition, the freshwater diversity of Pavlovophyceae was investigated by lineage-specific PCR-primers and clone library sequencing from another Norwegian lake, Lake Svaersvann. We present new freshwater phylotypes belonging to the classes Prymnesiophyceae and Pavlovophyceae, as well as a distinct group here named HAP-1. This is the first molecular evidence of a freshwater species belonging to the class Pavlovophyceae. The HAP-1 and another recently detected marine group (i.e. HAP-2) are separated from both Pavlovophyceae and Prymnesiophyceae and may constitute new higher order taxonomic lineages. As all obtained freshwater sequences of haptophytes are distantly related to the freshwater species C. parva, the phylogeny demonstrates that haptophytes colonized freshwater on multiple independent occasions. One of these colonizations, which gave rise to HAP-1, took place very early in the history of haptophytes, before the radiation of the Prymnesiophyceae.     

On the central nervous system of Smeagolidae and Rhodopidae, two families questionably allied with the Gymnomorpha (Gastropoda: Euthyneura)

The central nervous systems ( CNS ) of Smeagol manneringi Climo, 1980 (Smeagolidae), of Rhodope veranü Kölliker, 1847, and of Rhodope transtrosa Salvini-Plawén, 1989 are redescribed in detail. The smeagolid CNS exhibits diagnostic pulmonate characters (procerebrum, cerebral gland, dorsal bodies). Sharing a distinctly structured abdominal ganglion and other peculiarities, the Smeagolidae are closely related to the Onchidüdae, and both families are united as Onchidioidea. The consequences of this close relationship for the origin and evolution of the Gymnomorpha are discussed and the value of the pulmonate CNS for phylogenetics is reconsidered. On the basis of neural characters, which are correlated with the mode of breathing organs, the Pulmonata are divided into Basommatophora, Systellommatophora (Otinidae and Gymnomorpha) and Eupulmonata ( ord. nov .: Trimusculidae, Ellobüdae, Stylommatophora).
In contrast, the CNSs of the rhodopid species lack the pulmonate attributes, but show diagnostic opisthobranch characters such as a rhinophoral nerve. Accordingly, the Rhodopidae are excluded from the Pulmonata and are classified as a separate order Rhodopemorpha among the Opisthobranchia.     

Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.Subject terms: Phylogenetics, Microbial ecology