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Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, ‘ Candidatus Uab amorphum’, which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the ‘ Ca . Uab amorphum’ genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this “phagotrophic” bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells. Phagocytosis is a typically eukaryotic feature that could be behind the origin of eukaryotic cells. Here, the authors describe a bacterium that can engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism.

Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden–Meyerhof–Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.

Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics continues to evolve with the addition of new genomes. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n = 258), single-amplified genomes (n = 84), previously existing (n = 2), and new isolate genomes (n = 5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totaling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology.

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N 2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world’s largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth’s most abundant organismal group. Bacteria of the SAR11 clade constitute up to one half of all marine microbes and are thought to require oxygen for growth; here, a subgroup of SAR11 bacteria are shown to thrive in ocean oxygen minimum zones and to encode abundant respiratory nitrate reductases. An anoxic niche for SAR11 bacteria SAR11 bacteria, the most abundant type of microbe in the world's oceans, are thought to require oxygen for growth, yet they are also abundant in waters where oxygen levels are low. Frank Stewart and colleagues show here that a subgroup of SAR11 bacteria that thrives in ocean oxygen minimum zones have adapted to the microaerobic/anaerobic conditions there, and they encode abundant respiratory nitrate reductases that perform the first step in denitrification. These results redefine the ecological niche of Earth's most abundant organismal group and suggest that they are substantial contributors to nitrogen loss in oxygen minimum zones.

The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria. The Alphaproteobacteria form one of the most abundant groups of bacteria on Earth, and one that is closely linked to all complex forms of life. Many bacteria within this class live inside the cells of other organisms. For example, mitochondria – the powerhouses of animal, plant and other eukaryotic cells – evolved from bacteria within this group. Other alphaproteobacteria act as parasites or beneficial symbionts within cells. The history of life on Earth can be thought of as a tree, with each branch representing the evolution of a new species from a common ancestor. But for many bacteria, the earliest stages of their evolutionary history are so tangled and complex that their origin remains largely unknown. For example, efforts to study the earliest history of the Alphaproteobacteria have been plagued with errors and artefacts. The extreme variation in the genetic sequences of different bacteria in the group make it particularly challenging to uncover relationships between the species. To overcome this problem, Muñoz-Gómez et al. focused on a set of 200 genes that occur in all alphaproteobacteria, and used a range of strategies to reduce potential errors in the data. The results propose a new general structure for the evolutionary tree of the Alphaproteobacteria. This shows that two groups of alphaproteobacteria that were thought to be closely related to each other – the parasites Rickettsiales and Holosporales – are unrelated. Instead, these groups evolved independently from different free-living alphaproteobacteria. The abundance and diversity of the Alphaproteobacteria means that the improved understanding of their evolutionary origins could influence the work of a wide range of scientists. Further research could help to shed light on how parasitic bacteria interact with the cells they invade; reveal how bacteria evolved certain abilities, such as the ability to photosynthesize; and uncover the precise origin of mitochondria.

Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphapro teobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.

Elucidating the timescale of the evolution of Alphaproteobacteria , one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth’s systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria , based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales , an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited. Dating early bacterial evolution is challenging due to the limited bacterial fossil record. Here Wang and Luo use the close evolutionary relationship between Alphaproteobacteria and mitochondria to leverage the eukaryotic fossil record in dating Alphaproteobacteria origin and diversification.

Growth media have been developed to facilitate the enrichment and isolation of acidophilic and acid-tolerant sulfate-reducing bacteria (aSRB) from environmental and industrial samples, and to allow their cultivation in vitro. The main features of the ‘standard’ solid and liquid devised media are as follows: (i) use of glycerol rather than an aliphatic acid as electron donor; (ii) inclusion of stoichiometric concentrations of zinc ions to both buffer pH and to convert potentially harmful hydrogen sulphide produced by the aSRB to insoluble zinc sulphide; (iii) inclusion of Acidocella aromatica (an heterotrophic acidophile that does not metabolize glycerol or yeast extract) in the gel underlayer of double layered (overlay) solid media, to remove acetic acid produced by aSRB that incompletely oxidize glycerol and also aliphatic acids (mostly pyruvic) released by acid hydrolysis of the gelling agent used (agarose). Colonies of aSRB are readily distinguished from those of other anaerobes due to their deposition and accumulation of metal sulphide precipitates. Data presented illustrate the effectiveness of the overlay solid media described for isolating aSRB from acidic anaerobic sediments and low pH sulfidogenic bioreactors. The paper describes how bacteria that live in acidic environments, and that form hydrogen sulphide from sulfate, may be isolated and grown in the laboratory. Graphical Abstract Figure. The paper describes how bacteria that live in acidic environments, and that form hydrogen sulphide from sulfate, may be isolated and grown in the laboratory.

The degradation of particulate organic matter in the ocean is a central process in the global carbon cycle, the mode and tempo of which is determined by the bacterial communities that assemble on particle surfaces. Here, we find that the capacity of communities to degrade particles is highly dependent on community composition using a collection of marine bacteria cultured from different stages of succession on chitin microparticles. Different particle degrading taxa display characteristic particle half-lives that differ by ~170 h, comparable to the residence time of particles in the ocean’s mixed layer. Particle half-lives are in general longer in multispecies communities, where the growth of obligate cross-feeders hinders the ability of degraders to colonize and consume particles in a dose dependent manner. Our results suggest that the microscale community ecology of bacteria on particle surfaces can impact the rates of carbon turnover in the ocean. Particle-attached bacteria play a key ecosystem role by degrading complex organic materials in the ocean. Here, the authors use model marine microbial communities to show that community composition and interspecies interactions can significantly slowdown the rates of particle turnover in the environment.

Green Ulvacean marine macroalgae are distributed worldwide in coastal tidal and subtidal ecosystems. As for many living surfaces in the marine environment, little is known concerning the epiphytic bacterial biofilm communities that inhabit algal surfaces. This study reports on the largest published libraries of near full-length 16S rRNA genes from a marine algal surface (5293 sequences from six samples) allowing for an in-depth assessment of the diversity and phylogenetic profile of the bacterial community on a green Ulvacean alga. Large 16S rRNA gene libraries of surrounding seawater were also used to determine the uniqueness of this bacterial community. The surface of Ulva australis is dominated by sequences of Alphaproteobacteria and the Bacteroidetes , especially within the Rhodobacteriaceae , Sphingomonadaceae , Flavobacteriaceae and Sapropiraceae families. Seawater libraries were also dominated by Alphaproteobacteria and Bacteroidetes sequences, but were shown to be clearly distinct from U. australis libraries through the clustering of sequences into operational taxonomic units and Bray–Curtis similarity analysis. Almost no similarity was observed between these two environments at the species level, and only minor similarity was observed at levels of sequence clustering representing clades of bacteria within family and genus taxonomic groups. Variability between libraries of U. australis was relatively high, and a consistent sub-population of bacterial species was not detected. The competitive lottery model, originally derived to explain diversity in coral reef fishes, may explain the pattern of colonization of this algal surface.