Different Planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment

The Utility of Macroecological Rules for Microbial Biogeography

Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Bacterial community composition and diversity in the ballast water of container ships arriving at Yangshan Port, Shanghai, China

Ballast water is a major vector of invasion by protozoans and metazoans. Bacterial invasion is less-well understood. We surveyed the bacterial diversity of ballast water from 26 container ships arriving at the Yangshan Deepwater Port, Shanghai, China during 2015-2016. We characterized the ballast microbiome using high-throughput sequencing (HTS) based on V4-V5 region of 16S rRNA genes. We simultaneously monitored physicochemical parameters of the ballast water, including temperature, pH, dissolved oxygen (DO), salinity, turbidity, total suspended solid (TSS), particulate organic carbon (POC), NO₂, NH₄, PO₄. Proteobacteria was the dominant phylum, comprising more than 50% of the OTUs of almost all vessels, followed by Bacteroidetes (12.08%), Actinobacteria (4.86%) Planctomycetes (3.24%) and Cyanobacteria (1.95%). The relative abundance of Cyanobacteria differed among vessels. It was negatively correlated with temperature, NO₃, pH, TSS, PO₄, and turbidity and positively correlated with NH₄, POC. The genus Synechococcus was the most common Cyanobacteria in our results. Escherichia coli were relatively rare; they are indicator-species of D-2 standards published by the IMO. The relative abundance of the genus Vibrio ranged from 0.003% to 24.88% among different vessels. Our results showed that HTS was able to profile the bacterial communities in ballast-waters, even when the approach was restricted by technical and other obstacles.

Characterizing microbial diversity and community composition of groundwater in a salt-freshwater transition zone

A salt-freshwater transition zone due to seawater intrusion to groundwater promotes changes in microbial diversity and community composition in a coastal aquifer. The main purpose of this study is to explore the effect of seawater intrusion on the groundwater quality in a salt-freshwater transition zone and identify the microbial fingerprints of seawater intrusion. The changes in microbial community diversity response to the seawater intrusion were characterized by comparing the community structures of the microbes in fresh groundwater, seawater, and salty groundwater from various monitoring wells at different depths using the high throughput 16S rDNA gene sequencing. Results show that seawater had the lowest taxon richness and evenness, and the irrigation water had the highest richness and evenness. Statistical analysis showed that DO%, ORP, and Cl^- affected microbial distribution in the groundwater; while DO% was a main environmental factor influencing microbial community diversity. The analysis of microbial community structures indicates that the order Oceanospirillales and the family Alteromonadaceae could be used as indicators of seawater intrusion.

Improved culture of fastidious Gemmata spp. bacteria using marine sponge skeletons

Gemmata are Planctomycetes bacteria recalcitrant to traditional cultivation in the clinical microbiology laboratory and they have been seldom documented in patients. Based on previously known relationships of Planctomycetes with marine sponges, we designed a new culture medium A incorporating marine sponge skeleton of Spongia sp. to the standard culture medium; and culture medium B incorporating Spongia sp. skeleton heat aqueous filtrate into medium A; and inoculating the three culture media (standard, A and B) with Gemmata obscuriglobus DSM 5831^T and Gemmata massiliana DSM 26013^T in the presence of negative controls. Cultures were observed by naked eyes for 7 days and bacterial growth was quantified by microscopic observations and culture-based enumerations. Macroscopic observations at day-3 revealed a pink bacterial pellet in medium B tubes while standard medium tubes remained limpid until day-8. Growing Gemmata spp. bacteria in medium A yielded air bubbles released by bacterial respiration, whereas control tubes remained bubble-free. The number of colonies in standard medium (1.363 ± 115 for G. obscuriglobus, 1.288 ± 83 for G. massiliana) was significantly lower than those counted from medium B (2.552 ± 128 for G. obscuriglobus, 1.870 ± 112 for G. massiliana) and from medium A (2.851 ± 137 for G. obscuriglobus, 2.035 ± 163 for G. massiliana) (p < 0.10^-4) at day-2 incubation. At day-3 incubation, the number of colonies counted from supplemented media A and B increased up to one log than those counted from the control medium (p < 0.10^-4). Along the following day-4-7 incubation, the number of colonies counted from media A and B remained significantly higher compared to standard medium (p < 0.10^-4). These data indicate that incorporation of spongin-based marine sponge skeleton and heat aqueous filtrate of sponge skeleton significantly improved growth of Gemmata spp. bacteria. These observations pave the way towards improved isolation and culture of Gemmata spp. from environmental and clinical specimens.

Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific)

The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.

Development of a chemically-defined minimal medium for studies on growth and protein uptake of Gemmata obscuriglobus

We experimentally determined minimal media requirements for Gemmata obscuriglobus, a Gram-negative Planctomycete bacteria with several unusual physiological features. We find that supplementing media with the usual vitamins solution does not improve viability, but does result in an increased growth rate in liquid cultures and a larger colony size on agar plates. By systematically including individual vitamins, or omitting individual vitamins, from media we find that the addition of only two vitamins, biotin and cyanocobalamin, are sufficient to restore colony growth to comparable rates as other commonly used media. Overall, our findings define minimal media requirements for the culturing of this low-nutrient organism. One of G. obscuriglobus unusual physiological features is the ability to internalize fully-folded proteins. Using fluorescence microscopy and flow cytometery we show that this physiological behavior is dependent on media state and composition. The percentage of cells exhibiting internalization of GFP when grown on a particular, solid minimal medium is far greater than cells grown in liquid medium of similar composition or other solid media with different compositions.

Compartmentalization in PVC super-phylum: evolution and impact

BACKGROUND

The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes.

RESULTS

Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes.

CONCLUSIONS

Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences.

REVIEWERS

This article was reviewed by Mircea Podar and Olivier Tenaillon.

Gemmata species: Planctomycetes of medical interest

The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.

Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants

Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH 8, at 30 °C and salinity ≤ 1.25 % NaCl. G. massiliana is resistant to β-lactam antibiotics, due to lack of peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G. massiliana genome increases knowledge of a poorly known world of bacteria.

Community composition of the Planctomycetes associated with different macroalgae

Insights into the diversity of marine natural microbial biofilms, as for example those developing at the surface of marine macroalgae, can be obtained by using molecular techniques based on 16S rRNA genes. We applied denaturing gradient gel electrophoresis (DGGE) with 16S rRNA genes-specific primers for Planctomycetes to compare the communities of these organisms developing on six different macroalgae (Chondrus crispus, Fucus spiralis, Mastocarpus stellatus, Porphyra dioica, Sargassum muticum, and Ulva sp.) sampled in spring 2012 in two rocky beaches in the north of Portugal. Planctomycetes can be one of the dominant organisms found in the epibacterial community of macroalgae, and we wanted to determine the degree of specificity and the spatial variation of these group. Shannon diversity indexes obtained from the comparison of DGGE profiles were similar in all the macroalgae, and in both sites, F. spiralis was the algae presenting lower Planctomycetes diversity, while M. stellatus and P. dioica from Porto showed the highest diversity. The analysis of DGGE profiles, including anosim statistics, indicate the existence of a specific Planctomycetes community associated with the algal host, likely independent of geographical variation. Sequencing of DGGE bands indicated that Planctomycetes communities were highly diverse, and some Operational Taxonomic Units seemed to be specifically associated with each macroalgae.

Signature protein of the PVC superphylum

The phyla Planctomycetes, Verrucomicrobia, Chlamydiae, Lentisphaerae, and "Candidatus Omnitrophica (OP3)" comprise bacteria that share an ancestor but show highly diverse biological and ecological features. Together, they constitute the PVC superphylum. Using large-scale comparative genome sequence analysis, we identified a protein uniquely shared among all of the known members of the PVC superphylum. We provide evidence that this signature protein is expressed by representative members of the PVC superphylum. Its predicted structure, physicochemical characteristics, and overexpression in Escherichia coli and gel retardation assays with purified signature protein suggest a housekeeping function with unspecific DNA/RNA binding activity. Phylogenetic analysis demonstrated that the signature protein is a suitable phylogenetic marker for members of the PVC superphylum, and the screening of published metagenome data indicated the existence of additional PVC members. This study provides further evidence of a common evolutionary history of the PVC superphylum and presents a unique case in which a single protein serves as an evolutionary link among otherwise highly diverse members of major bacterial groups.

Diversity of Planctomycetes in iron-hydroxide deposits from the Arctic Mid Ocean Ridge (AMOR) and description of Bythopirellula goksoyri gen. nov., sp. nov., a novel Planctomycete from deep sea iron-hydroxide deposits

Planctomycetes form a deep branching and distinct phylum of the domain Bacteria, and represent a fascinating group due to their unusual features such as intracellular compartmentalization and lack of peptidoglycan in their cell walls. The phylum Planctomycetes was described already in 1924, but still the diversity of this phylum represents an enigma and unexploited resource. In this study the diversity of the phylum Planctomycetes in low temperature iron-hydroxide deposits at the Mohns Ridge, a part of the Arctic Mid Ocean Ridge (AMOR), was characterised by descriptive analysis of 16S rRNA gene sequences in combination with isolation of planctomycetes strains. The 16S rRNA gene sequences were affiliated with three order within the phylum Planctomycetes namely the (i)Planctomycetales, (ii) "Candidatus Brocadiales" and (iii) Phycisphaerae in addition to sequences affiliating to hitherto unknown Planctomycetes. The majority of the sequences were affiliated with the CCM11a group (Phycisphaerae), and with the Pir4 group (Planctomycetaceae). Two strains from the order Planctomycetales were isolated. One strain (Plm2) showed high similarity to the previously isolated Planctomyces maris (99 % 16S rRNA sequence identity). The other strain (Pr1d) belonged to the Pir4 group, and showed highest identity with Rhodopirellula baltica (86 %), Blastopirellula marina (86 %) and Pirellula staleyi (85 %). Based on its physiological and biochemical properties, strain Pr1d(T) is considered to represent a new genus of the order Planctomycetales. We propose to classify the novel planctomycete in a new genus and species, Bythoypirellula goksoyri gen. nov., sp. nov., the type strain being Pr1d(T).

Aquisphaera giovannonii gen. nov., sp. nov., a planctomycete isolated from a freshwater aquarium

As part of a study of the diversity of planctomycetes, two novel strains, designated OJF2T and OJF8, were isolated from the sediments of a freshwater aquarium. The organisms were chemoheterotrophic, spherical and pink-pigmented, had an optimum growth temperature of about 30–35 °C and an optimum pH for growth of around 7.5–8.5. The predominant fatty acids were C18 : 1ω9c and C16 : 0. The two strains were able to assimilate several sugars and organic acids. 16S rRNA gene sequence analysis confirmed the affiliation of these organisms to the phylum ‘Planctomycetes’; they showed highest similarity to the type strains of Singulisphaera acidiphila (92.4 %) and Isosphaera pallida (91.9 %). On the basis of physiological, biochemical and chemotaxonomic characteristics, strains OJF2T and OJF8 are considered to represent a novel species of a new genus of the order Planctomycetales, for which the name Aquisphaera giovannonii gen. nov., sp. nov. is proposed. The type strain of Aquisphaera giovannonii is OJF2T ( = CECT 7510T  = DSM 22561T).

Comparison of primer sets for the study of Planctomycetes communities in lentic freshwater ecosystems

In search of a primer set that could be used to study Planctomycetes dynamics in lakes and especially via fingerprinting methods, e.g. denaturing gradient gel electrophoresis (DGGE), three existing specific primer sets, developed for marine and soil systems, have been tested on water samples from four freshwater ecosystems. The first primer set (PLA46F/PLA886R) allowed PCR amplification of Planctomycetes sequences in only one of the four ecosystems, whereas the second primer set (PLA40F/P518R) amplified Planctomycetes sequences in all the studied ecosystems but with a low specificity, since sequences belonging to Verrucomicrobiales and Chlamydiales clades were also amplified. Finally, the third primer set (PLA352F/PLA920R) allowed amplification of Planctomycetes sequences in the four ecosystems with a very high specificity. It amplified all known Planctomycetes genera and yielded the highest Operational Taxonomic Unit (OTU) richness and diversity estimates. In silico analyses supported these results. Further experiments comparing PLA352F/PLA920R to PLA46F/P1390R (a primer set generating a longer PCR fragment, also used to study Planctomycetes) yielded very similar results. Our findings suggest that the primer set PLA352F/PLA920R provides good estimates of Planctomycetes richness and diversity compared with other, and can thus be used to study Planctomycetes dynamics in lentic freshwater ecosystems.