Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

doi:10.21203/rs.2.20535/v2

Download PDF

Research

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

https://doi.org/10.21203/rs.2.20535/v2

This work is licensed under a CC BY 4.0 License

Journal Publication

published 31 Aug, 2020

Read the published version in Microbiome →

You are reading this older preprint version

Read the latest preprint version →

Background: Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ- Proteobacteria . Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales ), the predatory and living strategies of Bradymonadales are still largely unknown. Results: Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes . Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual-transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. Conclusions: Bradymonabacteria have unique living strategies that differ from those of so-called “obligate” or “facultative” predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, (ii) facultatively prey-dependent predators, and (iii) prey-independent predators. Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments.

General Microbiology

Bacterial predator

Bradymonadales

Metabolic deficiencies

Comparative genomic analysis

Biogeographic analysis

Bacterial predators have been proposed as an indispensable selective force in bacterial communities [1-4]. Predation by bacteria can release nutrients [5] and affect biogeochemical cycling. In contrast to phages, bacterial predators do not need to be present in high concentrations to drive significant bacterial mortality in the environment [6, 7]. In addition, bacterial predators have higher prey-killing efficiency in low-nutrient medium than phages [8]. However, these studies have mostly been based on Bdellovibrio and like organisms (BALOs), and little is known of the ecological roles of other bacterial predators.

Predatory bacteria are classified into two categories, obligate or facultative predators, based on their prey-independent or prey-dependent living strategies [9]. Obligate predators include several genera collectively known as BALOs [10]. These predatory bacteria can attack their prey by penetrating the cell wall [11], dwelling in the periplasm and then killing their host [12]. Therefore, their lifestyle depends on the presence of their prey in the environment, and BALOs lose viability within several hours if prey is not available [8, 13]. Facultative predators also include several genera [9], such as Myxococcus, Lysobacter, and Herpetosiphon [14]. These predators kill their prey by secreting antimicrobial substances into the surrounding environment [9]. In general, facultative predators have been considered those that can be maintained as pure bacterial cultures. However, obligate predators can also be grown as pure cultures on complex microbial extract-based media [15]. Indeed, most so-called obligate predators have a host-independent lifestyle [12, 16]. As a result, the definition “obligate predator” does not fully describe their lifestyle. Thus, it is necessary to develop a different framework to categorize the currently known bacterial predators.

Bradymonabacteria are representative of the novel order Bradymonadales, which are phylogenetically located in the δ-Proteobacteria [17]. The first type species of Bradymonadales, Bradymonas sediminis FA350^T, was isolated in 2015 [17]. To date, 9 strains within the Bradymonadales have been isolated and found to belong to 7 candidate novel species; these Bradymonabacteria are bacterial predators [18]. Interestingly, the phylum Proteobacteria contains three orders of predatory bacteria. Among them, Myxococcales and Bradymonadales belong to δ-Proteobacteria, while Bdellovibrionales were classified as Oligoflexia in 2017 [19]. Myxococcales and Bdellovibrionales are facultative and obligate predators, respectively. Additionally, they have different distribution patterns in the environment. Myxococcales are mainly found in soil and sediment niches [20, 21], while Bdellovibrionales are aquatic. However, how Bradymonadales adapt to predatory lifestyles and whether they have specific living strategies or ecological importance remain largely unknown.

Here, we analyzed the predation range of Bradymonadales on diverse bacteria and their predatory morphological and physiological characteristics. By using comparative genomic analysis of Bradymonadales and other predatory bacteria, we revealed the genetic and metabolic potential of this group. To assess the diversity and frequency of occurrence of the various ribotypes of known predators (Bradymonadales, Myxococcales and Bdellovibrionales) on a global scale, we surveyed published 16S rRNA gene amplicon datasets from a number of ecosystems representing a broad range of geographic locations, climatic zones, and salinities. Our study provides an ecological and evolutionary framework for Bradymonadales and highlights their potential ecological roles in predation.

Bradymonabacteria are efficient predators of diverse prey bacteria

In total, 9 strains of bacteria in the novel order Bradymonadales were isolated using the enrichment culture method [22]. Among these strains, FA350^T [17, 18] and B210^T [23] were the two type strains for different genera in Bradymonadales. Both these type strains were used to investigate the predator-prey range of Bradymonabacteria. A total of 281 isolated bacteria were cocultured with Bradymonabacteria FA350^T [17, 18] or B210^T [23] as lawns in individual Petri dishes (Fig. 1a, Table S1). Zones of predation were measured (Fig. 1b), and the results showed that the Bradymonabacteria preyed on diverse bacteria but showed a strong preference for Bacteroidetes (90% of tested bacteria could be preyed on) and Proteobacteria (71% of tested bacteria could be preyed on) (Fig. 1c). Predation on bacteria in the orders Flavobacteriales, Caulobacterales, Propionibacteriales, and Pseudomonadales was broadly distributed, with a mean predation percentage greater than 90%, while predation of Micrococcales and Enterobacteriales was less efficient.

Transmission electronic microscopy (TEM) and scanning electronic microscopy (SEM) analyses were performed to understand the mechanism of predation of strain FA350^T on the subcellular level. Lysis of the prey cells was detected near strain FA350^T in both the TEM and SEM analyses (Fig. 2). Strain FA350^T was found to have pili (Figs. 2b and 2g) and outer membrane vesicle (OMV)-like structures (Figs. 2d, 2e, 2f, and 2h). In addition, FA350^T cells contained intracellular particles with low electron density (Figs. 2b, 2c, 2d, and 2f), which were shown to contain polyhydroxyalkanoates (PHAs) by Nile blue A staining. FA350^T cells also contained several electron-dense (black) spots (Figs. 2b, 2c, 2d, and 2f), which indicated the presence of intracellular polyphosphate granules [24]. Both of these particle types significantly accumulated during predation (Fig. 2).

Bradymonabacteria are polyauxotrophs

To explore the metabolic capabilities and predation mechanism of this novel group, we analyzed 13 genomes of Bradymonadales (9 high-quality genomes sequenced from cultured strains and 4 reconstructed from published studies [25]). The genome size of Bradymonabacteria ranged from 5.0 Mb to 8.0 Mb. Average nucleotide identity (ANI) analysis of the 9 cultured strains of Bradymonadales revealed 7 different species [26] (Fig. S1b). Other general features of the genomes are described in the Supplementary Materials (Supplementary Materials Results and Fig. S1a).

Almost all strains (except FA350^T) possessed a minimal pentose phosphate pathway, which lacked key steps for the synthesis of ribose 5-phosphate (Fig. 3, Table S2) [27]. Most of the bradymonabacterial genomes lacked key enzymes for pyrimidine synthesis, such as aspartate carbamoyltransferase, which catalyzes the first step in the pyrimidine biosynthetic pathway. All genomes lacked the complete purine de novo pathway; they were missing the phosphoribosylaminoimidazole carboxylase catalytic subunit or even the whole pathway.

In addition to this auxotrophy in the synthesis of pentose and nucleotides, all the genomes lacked complete pathways for the synthesis of many amino acids, such as serine, methionine, valine, leucine, isoleucine, histidine, tryptophan, tyrosine, and phenylalanine (Fig. 3). For example, all the genomes encoded a potential D-3-phosphoglycerate dehydrogenase for the conversion of glycerate-3P into 3-phosphonooxypyruvate for amino-acid synthesis (Fig. 3). However, in all members of Bradymonabacteria, this pathway appeared to be blocked at the subsequent step because of the absence of phosphoserine aminotransferase, although Bradymonabacteria could continue with subsequent pathways to complete the biosynthesis of cysteine and glycine. Additionally, many cofactors and vitamins that promote bacterial growth [22], such as biotin, thiamin, ubiquinone, VB₁₂, and VB_6,could not be synthesized by the de novo pathway in almost all the genomes. Notably, all the genomes had an incomplete pathway for type II fatty acid biosynthesis, lacking the key enzymes 3-oxoacyl-[acyl-carrier-protein] synthase I/II (FabB/F) and enoyl-[acyl-carrier-protein] reductase (FabI/L).

Dual-transcriptome analysis of the potential predation mechanism of Bradymonabacteria

To further determine the genes involved in predation, we performed dual-transcriptome analysis of Bradymonas sediminis FA350^T with and without preying on Algoriphagus marinus am2 (Fig. S2). As with obligate predators, one way that Bradymonabacteria kill their prey bacteria is likely by using contact-dependent mechanisms. Here, the bradymonabacterial genomes possessed complete Type IV pili (T4P) (Fig. 3), and the attached areas showed more type IV pili than the unattached areas (SEM, Figs. 2g and 2h). The dual-transcriptome analysis showed that genes encoding the type IV pili twitching motility protein PilT (DN745_17255) were significantly upregulated during predation (Fig. S3), suggesting that these genes may be involved in predation. Bradymonabacteria also had T4b pilins showing homology to those in Bdellovibrio bacteriovorus HD100, in which T4b pilins are necessary for predation [28, 29] (Fig. S4), so T4b pilins may also participate in regulating predation in Bradymonabacteria. In addition, this group of bacteria had type II and type III secretion systems (the YscRSTUV proteins that form a membrane-embedded complex known as the ‘‘export apparatus’’ [30]). The dual-transcriptome analysis also supported the prediction that genes encoding the type III secretion system inner-membrane protein complex (DN745_01900, DN745_10315, DN745_17280, DN745_03325, and DN745_00480) were significantly upregulated during predation (Fig. S3), implying that these genes may also be involved in predation.

Another way that Bradymonabacteria kill their prey bacteria is likely by secreting antimicrobial substances into the surrounding environment. As in most facultative bacterial predators, a few potential antimicrobial clusters of secondary metabolite synthesis, such as Lasso-peptide [31], were found in almost all genomes of Bradymonabacteria (Fig. 3). Genes involved in OMV-like biosynthesis were also detected in most genomes, such as ompA (cell envelope biogenesis protein), envC (Murein hydrolase activator) and tolR (envelope stability) [32]. Vesicle membrane-related genes (DN745_03865, DN745_02930, and DN745_07125) were significantly upregulated during predation (Table S4, Fig. S3).

Bradymonabacteria are novel predators different from obligate or facultative predators

Comparative genomic analysis with other bacterial predators was performed to explore whether Bradymonabacteria have a unique living strategy. Two-way cluster analysis showed that bradymonabacterial genomes contained features different from those of either obligate or facultative predators, which were phylogenetically located in a different branch (Fig. 4). The specific multiple metabolic deficiencies of Bradymonabacteria had some similarities to those of most obligate predators. For example, both Bradymonabacteria and obligate predators possessed a minimal pentose phosphate pathway, lacked key enzymes for pyrimidine synthesis, and lacked complete pathways for the synthesis of many amino acids, cofactors, and vitamins (Fig. 4). However, Bradymonabacteria with multiple auxotrophies could grow on common media (such as marine agar medium), though at a low growth rate [33], unlike obligate predators.

Unlike most obligate predators, the polyphosphate accumulation pathway, containing a pair of genes (Polyphosphate kinase and Exopolyphosphatase) associated with both polyphosphate formation and degradation [34], was present in most Bradymonabacteria (Fig. 4). Polyphosphate accumulation was also detected in FA350^T cells during predation (Fig. 2). In contrast to most of the other predator genomes, potential PHA synthesis from β-oxidation of fatty acids [35] was observed in most bradymonabacterial genomes (Fig. 3). In this study, TEM analysis showed that strain FA350^T could significantly accumulate PHAs during predation compared with pure culture (Fig. 2). Despite their incomplete fatty acid biosynthetic pathway, all Bradymonabacteria had a high copy number of long-chain fatty acid transporters (fadL) compared to those of other predators, allowing them to gather fatty acids from the environment (Fig. 4). In addition, genes associated with alkane synthesis, which is important for maintaining cell membrane integrity and adapting to cold environments [36], were present in most genomes of Bradymonabacteria (Figs. 3 and 4). Thus, we proposed that Bradymonabacteria could be categorized as novel predators different from so-called obligate or facultative predators (Table 1).

Bradymonadales are mainly distributed in saline environments with high diversity

To evaluate the global prevalence of the Bradymonadales order, we surveyed recently published 16S rRNA gene amplicon studies that provided high taxonomic resolution along with relative sequence abundances. The 16S rRNA gene amplicons from 1552 samples were grouped into eight types of environments (Fig. 5a and Table S5). A total of 811 samples were from inland environments, while others were from marine environments, with each biotope showing a somewhat different microbial community (Figs. 5b and S5). Bradymonabacteria was detected in 348 of 741 marine samples (relative abundance>0.01%) but only 20 of 544 soil samples (Fig. 5a). All samples were sorted into an ordination diagram based on the similarity of communities (Fig. 5b). Saline biotopes were clearly separated from nonsaline biotopes (Fig. S6), suggesting that salinity was a significant factor in shaping microbial communities. For each biotope, the relative abundance of Bradymonadales in the saline environments (i.e., seawater and saline lake sediment) was significantly higher than that in the nonsaline environments (i.e., nonsaline soil and nonsaline water) (P<=0.0001, Fig. 5c). The distribution analysis was consistent with the genomic feature analysis (Fig. 2), in which several genes encoding sodium symporters and Na⁺/H⁺antiporters were found in the genomes, suggesting a beneficial effect of salinity on Bradymonabacteria.

In addition, we compared the relative abundance of Bradymonadales with those of two orders of well-known predatory bacteria, Bdellovibrionales and Myxococcales [12, 37, 38]. We found that Myxococcales and Bdellovibrionales were also globally distributed (Fig. S7); however, Myxococcales were more commonly distributed in soil and sediment environments, while Bdellovibrionales were more likely to be found in freshwater and seawater (Fig. S7). The total relative abundances of Bradymonadales, Bdellovibrionales, and Myxococcales ranged from 0.7% to 6.4% of the total prokaryotic microbes in all 1552 samples (Fig. S8a). The mean relative abundance of Bradymonadales (0.51%) was similar to that of Bdellovibrionales (0.62%) when both were detected in environmental samples (Fig. S8b). In contrast, Bradymonadales was one of the most abundant known predatory bacteria in saline lake sediment and saline lake water (Fig. S8c).

To further determine how salinity affected the relative abundance of Bradymonadales, we used the Gaodao multipond salterns as a model and applied 16S rRNA gene amplicon, fluorescence in situ hybridization (FISH), and real-time PCR analyses (Figs. S8d and S9). The results showed that Bradymonadales appeared in all the tested multipond saltern datasets, accounting for an average of 0.74% of all bacterial sequences and more than 1.0% relative abundance within the range of 80 g/L and 265 g/L salinity (Fig. S8d), significantly higher than those of Bdellovibrionales and Myxococcales. Detailed descriptions of the effects of salinity on the abundance of Bradymonadales are provided in the supplementary materials (Supplementary Materials: Results, Figs. S8d and S9).

To explore the diversity and distinct evolution of bradymonabacterial subgroups in different biotopes, we performed a phylogenetic analysis of nearly full-length 16S rRNA gene sequences of diverse origin by maximum likelihood inference (Table S6). A total of 187 OTUs were detected and found to form six sequence clusters (Fig. 6a). Almost 87.2% of the representative sequences originated from saline biotopes (such as seawater, marine sediments, salterns, corals, and saline lakes). Since bradymonabacterial subgroups may be selectively distributed in local biotopes, we investigated the relative abundance of each subgroup throughout the 127 representative samples in which the relative abundance of Bradymonadales was above 1% (Fig. 6b). Five of the 6 bradymonabacterial subgroups showed significantly higher abundance in saline environments. Cluster-2 and cluster-6 were mainly observed in seawater biotopes, whereas cluster-3 was mainly observed in marine sediment and saline lake sediment (Fig. 6b), consistent with the environments of the cultured strains. Cluster-5 lineages tended to occur in both freshwater and seawater biotopes (Fig. 6b).

In all ecosystems, predation is an important interaction among living organisms. Bacterial predators are proposed to play an important role in controlling and shaping bacterial populations in diverse environments [3, 39]. However, despite their ecological importance, only a few examples of predatory bacteria have been studied in depth. Recently, many predatory bacteria from various phyla have been isolated from different environments; however, most of their predatory lifestyle strategies and adaptations remain unclear. This study systematically analyzed the predatory lifestyle adaptations, global distribution, and diversity of Bradymonadales; highlighted the ecological role of Bradymonadales; and provided a framework for the categorization of the known predatory bacteria.

In our study, based on comparative genomic and physiological analyses, Bradymonabacteria were shown to be a novel group of bacterial predators with versatile survival strategies different from those of either so-called “obligate” predators or “facultative” predators (Table 1). Furthermore, Bradymonabacteria had multiple metabolic deficiencies. Their incomplete pathways might be important for prey-dependent growth, as the precursor compounds could be acquired from predation. In addition, the loss of genes in the fatty acid biosynthetic pathway was notable, because fatty acids are integral components of the cellular membrane, and their synthesis is considered to be a housekeeping function of cells [40]. Thus, these organisms may incorporate exogenous fatty acids from prey bacteria into their membrane phospholipids using their high copy number of long-chain fatty acid transport proteins [41] (Fig. 3). The gene loss in these organisms may render them dependent on prey for their lost metabolic functions and may also provide a selective advantage by conserving predators’ limited resources [42]. However, the sequenced genomes of Bradymonabacteria were surprisingly large (5.0 Mb to 8.0 Mb, Fig. S1a), suggesting that Bradymonabacteria are far from obligate parasites, with seemingly none of the reductive evolution that results from a parasitic lifestyle in bacteria such as Mycobacterium leprae [43]. The large size of their genomes may be indicative of the vast range of genes required for Bradymonabacteria to both effectively tolerate the absence of prey and carry out predation.

In contrast to most predators, Bradymonabacteria can synthesize many nutrient polymers, such as polyphosphate, PHA, and alkane molecules. Exopolyphosphatase catalyzes the hydrolysis of terminal phosphate residues from polyphosphate chains, accompanying the production of ATP and thus playing a role in the production of energy [44]. Bradymonadales cells may accumulate polyphosphate in the phosphate-rich zone, using it as an energy source [45]. Meanwhile, PHA granules are synthesized as sinks of excess carbon and are used as carbon and energy reserves in starvation conditions [46]. Under nutrient starvation, maintenance energy and free amino acids can be provided by endogenous substrates such as PHAs and polyphosphate [47, 48]; this ability may be an important feature for the survival of Bradymonabacteria during intervals without predation. This feature is interesting among bacterial predators, as it is commonly found in animal predation. For example, the bear can store fat in its body to ensure that it will survive the long winter. In addition, Bradymonabacteria may also synthesize alkanes to maintain cell membrane integrity [36] and complement its poor fatty acid synthesis ability. Thus, these multiple auxotrophies and nutrient synthesis polymers confer on Bradymonabacteria a versatile survival strategy for natural environments, in contrast to the currently known obligate or facultative predators.

As bacterial predators, Bradymonabacteria have developed a wide range of mechanisms to attack their prey. Contact-dependent predation mechanisms allow predators to attach to the prey and then carry out predation. This process has a relatively low energy cost and could prevent secretory virulence factors from being diluted by the surrounding environment [49]. Bradymonabacteria also has T4P, which could pull adherent bacteria into close association with other bacteria [50]. T4P could also transport bound substrates such as DNA [51] into the periplasm and export exoproteins across the outer membrane [52]. Contact-dependent Type III secretion systems have also been found in Bradymonabacteria and are reported to be capable of moving virulence factors across bacterial outer membranes and directly across the host cell membrane into the cytoplasm of a host cell [53]. However, no reports have indicated that the type III secretion system is involved in direct combat between bacteria. Whether type III secretory complexes could penetrate the bacterial cell wall is unknown. Further gene knockout experiments and systematic TEM analysis should be performed to identify whether and how the type III secretion system works during predation.

Our biogeographic analysis suggested that Bradymonabacteria are mainly distributed in saline environments, and some other studies have also detected Bradymonadales in hypersaline soda lake sediments [25], suggesting that saline environments could be enriched in these bacteria. Our genome analysis also showed that Bradymonadales had many genes encoding sodium symporters and Na⁺/H⁺antiporters to maintain osmotic pressure in saline environments. These findings supported the global analysis (Figs. 5 and S8c), suggesting that Bradymonadales might be a dominant bacterial predator in some specific saline environments compared with Bdellovibrionales and Myxococcales. The analysis of the complex intragroup phylogeny of the 6 subgroups of Bradymonabacteria revealed that distinct evolutionary bradymonabacterial subgroups had arisen in different biotopes, suggesting the occurrence of adaptive evolution specific to each habitat. Patterns related to salinity status also suggest that most Bradymonadales are halophiles [17].

Bradymonabacteria had a very high predation efficiency on bacteria within the phylum Bacteroidetes. Members of the phylum Bacteroidetes are one the most abundant groups of bacteria in the ocean. Bacteroidetes are assumed to attach to particles and degrade polymers and have an important role in the carbon cycle of oceans [54]. Thus, a high predation efficiency of Bacteroidetes might provide Bradymonabacteria with important roles in regulating Bacteroidetes communities and affecting the carbon cycle of the oceans. In addition, Bradymonadales were detected in coral samples, as Bradymonabacteria have a wide range of prey, including the coral pathogen Vibrio harveyi, suggesting that Bradymonabacteria may protect coral hosts by consuming potential pathogens [39]. The exact ecological roles of this group in different environments should be determined in further studies.

The unique metabolic pathways of Bradymonabacteria, which include conspicuous metabolic deficiencies similar to those of obligate predators but with a more effective starvation stress response mechanism, provide these bacteria with a unique survival strategy (different from the survival models of so-called “obligate” or “facultative” predators). We propose a framework to categorize the current bacterial predators into 3 groups: (i) highly prey-dependent predators, such as most of the BALOs; (ii) facultatively prey-dependent predators, such as Bradymonabacteria; and (iii) prey-independent predators, such as Myxobacteria and Lysobacter sp. (Table 1). This categorization is helpful for further study of the different ecological importances of each type of bacterial predator. The evolution of bacterial predation in these three groups of predators should also be studied in the future to better understand the significance of predation to biological evolution.

Our study highlights the ecological role of Bradymonadales in saline environments. Given their substantial sequence and cell frequencies in the saline environment and their storage of nutrients as polymers in cells during predation, Bradymonadales may have an alternative way of regulating global nutrient cycling. To better understand the impact of bradymonabacterial predation on regulating biogeochemical cycling, predation mutants and microcosms need to be developed in further studies.

Predation experiments

To explore the predation of Bradymonabacteria, we used Bradymonas sediminis FA350^T and Lujinxingia litoralis B210^T as representative strains. All candidate prey strains were obtained from our laboratory. Cells were centrifuged, washed and concentrated in sea water to a final OD₆₀₀ of 3.0 for predator strains and 6.0 for candidate prey strains. Drops of 5.0 μl of the predator strain suspensions were deposited on the surfaces of agar plates and allowed to dry. Next, 20.0 μl drops of each different candidate prey strain suspension were placed near the predator spot. The plates were incubated at 33 °C, and images were taken after 48 h with a digital camera. To detect PHA accumulation, the granules were stained with the Nile red component of Nile blue A.

Genome sequencing and comparative genome analyses

To explore the potential metabolic capacity of bacterial predators, we sequenced 3 complete genomes and 6 draft genomes of all currently known Bradymonabacteria isolate strains using the methods reported in our previous studies [18, 55]. We also retrieved 37 predator genomes from NCBI (including 4 metagenome assembled genomes). tRNA and gene prediction were performed using tRNAscan and prodigal, respectively. The genome-based metabolic potential of the bacterial predators was predicted by BlastKOALA (https://www.kegg.jp/blastkoala/). The average nucleic acid identities among the 9 cultured Bradymonabacteria strains were calculated using pyani (https://github.com/widdowquinn/pyani), and the percentage of conserved proteins (POCP) in each strain was calculated as described previously by Qin et al.[56]).

Electronic microscopy analyses

We selected Algoriphagus marinus am2, which is smaller than the predator Bradymonas sediminis FA350^T, as prey. Bradymonas sediminis FA350^T and Algoriphagus marinus am2 were cultured separately to the exponential growth phase, adjusted to the same OD value, mixed together and cocultured on marine agar medium at 33 °C for 68 h.

For TEM analysis, mixed culture samples were supported on carbon/formvar-coated copper grids. The grids were inverted over a drop of 1% uranyl acetate. Thin sections were prepared with the predator-prey cocultures at 68 h incubation. The samples were mixed with 0.5 ml of 2% glutaraldehyde in 0.1 M sodium cacodylate buffer, centrifuged and resuspended in 1 ml of the same solution for 3 h. The cells were washed in cacodylate buffer, fixed with 1% osmium tetroxide and encased in agar. The agar-encased cells were then fixed in 2% uranyl acetate, dehydrated through an ethanol series and embedded in Epon resin. Thin sections were cut and stained with uranyl acetate and lead citrate. Specimens were examined with a JEM-1200EX electron microscope operated at 80 kV.

For SEM analysis, mixed culture samples were washed 3 times with PBS and fixed for 1 h in 2.5% glutaraldehyde in sodium cacodylate buffer (0.1 M, pH 7.2). To dehydrate the bacteria, the EM grids underwent a series of washes in increasing concentrations of ethanol (25, 50, 75, and 96%) and placed in a vacuum overnight. The samples were coated with gold and observed using a Nova NanoSEM 450.

Dual transcriptomic analyses

To determine the gene expression profiles of the type strain FA350^T, a pure culture of FA350^T and a coculture of FA350^T with the prey Algoriphagus marinus am2 were cultured on marine agar medium at 33 °C for 0 h, 68 h, and 120 h, respectively. Each time point was collected in triplicate (n=3) for further transcriptomic analysis. For the transcriptomic analysis, the RNA extraction, library construction, sequencing and analysis were performed as described in our previous study [57]. Sequencing was carried out on a HiSeq sequencer at Novogene Co., Ltd. (Beijing, China). For transcriptomic analysis of mixed culture samples (dual transcriptomic analysis), total RNA sequences were mapped to the complete genome of FA350^T using the method reported by Westermann et al. [58]. Then, the completely mapped sequences were selected for further analysis.

Phylogenetic analysis of bradymonabacterial type IV pili

An unrooted, maximum likelihood phylogeny shows relationships between the type IVa, type IVb, and type IVc pili and the archaellum (archaeal flagellum) and the T2SS and T4SS extension ATPases. The protein amino-acid sequences were aligned with mafft and used to estimate a maximum likelihood phylogeny with RAxML under the JTT substitution model with gamma-distributed rate variation. The protein amino-acid sequences of Bradymonas were annotated by RAST (Rapid Annotation using Subsystem Technology) [59]. The other protein amino-acid sequences were obtained from other research supplementary materials [60].

Biogeographic distribution database construction

All the 16S rRNA gene sequences analyzed in this paper were downloaded from the European Nucleotide Archive (https://www.ebi.ac.uk/ena, ENA) during or before December 2018. As a result, we collected 1,552 samples from 102 projects or studies: 25 from nonsaline lake sediments (NSLS), 275 from marine sediments (MS), 499 from nonsaline soil (NSS), 45 from saline soil (SS), 216 from nonsaline water (NSW), 19 from saline lake sediments (SLS), 466 from sea water (SW), and 7 from saline lake water (SLW) (Table S5).

Microbial community composition

The raw 16S rRNA gene reads were filtered with UCHIME. Quality filtering, chimera detection, dereplication, clustering into OTUs and assigning taxonomic information were performed using VSEARCH [61]. The SILVA database Ref_SSU release 132 was used as a reference taxonomic database (https://www.arb-silva.de/). Alpha diversity indices (Shannon, Simpson, Good’s coverage and Ace) detailing the microbial community composition within each sample were calculated using scikit-bio (http://scikit-bio.org/) in Python, and alpha diversity indices (Chao1) were calculated using the package fossil (https://www.rdocumentation.org/packages/fossil) in R. For estimating community dissimilarities, Bray-Curtis distance was calculated by vegan in R based on the relative abundance of each taxon at the order level.

Phylogenetic analyses

Both RAxML [62] and FastTree [63] were employed to construct the Bradymonabacteria phylogenetic tree. Given both the topology of the phylogenetic tree and its good coverage of all Bradymonabacteria lineages, we established the phylogenetic tree using 187 representative Bradymonabacteria 16S rRNA gene sequences, which were all longer than 1200 bp (at 98.5% cutoff). These sequences were aligned using mafft. The Bradymonabacteria subgroup designations were confirmed when one subgroup with > 10 representative sequences was monophyletic by two phylogenetic trees constructed by different programs using the maximum likelihood approach [64]. The environmental type (i.e., saline and nonsaline) of each Bradymonabacteria sequence in the tree was collected from GenBank. A genome-based phylogeny of bacterial predators and 9 cultured Bradymonabacteria strains was constructed using core genes [65], and trees were constructed using RAxML [62]. All phylogenetic trees were drawn using ggtree [66] in R.

Quantitative real-time PCR

The environmental DNA samples extracted in the previous step were used for qPCR experiments in order to detect the abundance of bacteria and Bradymonadales in each sample. The primer pair composed of 341F (5′-CCTACGGGAGGCAGCAG-3′) and 534R (5′-ATTACCGCGGCTGCTGGCA-3′) was used for quantification of bacteria [22]. A Bradymonadales-specific primer set composed of qBRA1295F (5′-CTCAGTTCGGATYGYAGTCTG-3′) and qBRA1420R (5′-GTCACCGACTTCTGGAGCAARCG-3′), which was designed in this study and generated an amplicon of 148 bases, was used for quantification of Bradymonadales. Reactions for each sample were carried out in an ABI StepOnePlus thermal cycler under the following conditions: an initial denaturation step at 95 °C for 10 min and then 40 cycles of 15 s at 95 °C and 30 s at 60 °C. The reaction were performed in a total volume of 20 μl, composed of 10 μl 2X Universal SYBR Green Fast qPCR Mix (ABclonal), 0.4 μl of each primer (10 μM), 1 μl of sample and 8.2 μl of MiliQ water. The Plasmid DNA Standard was constructed by introducing the 16S rDNA gene amplified from Bradymonas sediminis FA350^T into the pMD18-T Vector (TaKaRa) following the manufacturer’s instructions. The plasmid was isolated and purified using a MiniBEST Plasmid Purification Kit (TaKaRa). DNA copy number was determined by the concentration and relative molecular weight of the Plasmid DNA. For each QPCR assay, the plasmid aliquot was serially diluted to produce concentrations ranging from 10⁹ to 10³ DNA copies/μl to generate calibration curves. Each sample was measured in triplicate, and negative controls (no template NTC) were included.

Ethics approval and consent to participate

Not applicable

Consent for publications

Not applicable

Data availability

The genomes of cultured Bradymonabacteral isolates have been deposited in the NCBI database under GenBank accession numbers CP042467.1 (Bradymonadales sp. V1718), CP042468.1 (Bradymonadales sp. YN101), VOPX00000000.1 (Bradymonadales sp. TMQ1), VOSL00000000.1 (Bradymonadales sp. TMQ2), QRGZ00000000.1 (Bradymonadales sp. TMQ3), VOSM00000000.1 (Bradymonadales sp. TMQ4), CP030032.1 (Bradymonas sediminis FA350^T), QHKO00000000.1 (Lujinxingia litorali B210^T) and SADD00000000.1 (Lujinxingia sediminis SEH01^T). The genomes of uncultured Bradymonabacteria have been deposited in the NCBI database under GenBank accession numbers PWKZ00000000.1 (Bradymonadales bin CSSed10_215), PWTN00000000.1 (Bradymonadales bin CSSed11_191), PXAJ00000000.1 (Bradymonadales bin T3Sed10_204) and PWZZ00000000.1 (Bradymonadales bin T3Sed10_190). The 16S rRNA gene data sets of Gaodao salterns have been deposited in the Sequence Read Archive under accession number SRP217756 for all the samples. The transcriptome sequences for predation of FA350^T have been deposited in the NCBI database under accession numbers PRJNA559243 and PRJNA559253. All Bradymonabacteral isolates have been deposited at the Shandong Infrastructure of Marine Microbial Resources hosted by the Laboratory of Marine Microbiology at Shandong University (http://www.sdum.wh.sdu.edu.cn/search.html?itemId=14). Any Bradymonabacteral isolate is available upon request.

Competing interests

No conflict of interest exists in the submission of this manuscript, and the manuscript has been approved by all authors for publication. The authors declare that they have no competing interests.

Authors’ contributions

DSM, GJC, JZ, and ZJD designed the study. SW carried out TEM, SEM, and transcriptome analyses. ZZD carried out FISH and real-time PCR analysis. DSM, QYL, SW, XPW, and RT performed bioinformatic analyses. DSM and ZJD analyzed data and wrote the paper. JYN, AZ and YY improved the paper writing. All authors read and approved the manuscript

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31770002 and 41876166), Science and Technology Basic Resources Investigation Program of China (2017FY100302).

Young KD. The selective value of bacterial shape. Microbiol Mol Biol R. 2006;70(3):660-703.
Chauhan A, Cherrier J, Williams HN. Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle. P Natl Acad Sci USA. 2009;106(11):4301-6.
Johnke J, Cohen Y, de Leeuw M, Kushmaro A, Jurkevitch E, Chatzinotas A. Multiple micro-predators controlling bacterial communities in the environment. Curr Opin Biotech. 2014;27:185-90.
Li HH, Chen C, Sun QP, Liu RL, Cai JP. Bdellovibrio and Like Organisms Enhanced Growth and Survival of Penaeus monodon and Altered Bacterial Community Structures in Its Rearing Water. Appl Environ Microb. 2014;80(20):6346-54.
Martinez V, Jurkevitch E, Garcia JL, Prieto MA. Reward for Bdellovibrio bacteriovorus for preying on a polyhydroxyalkanoate producer. Environmental Microbiology. 2013;15(4):1204-15.
Richards GP, Fay JP, Dickens KA, Parent MA, Soroka DS, Boyd EF. Predatory Bacteria as Natural Modulators of Vibrio parahaemolyticus and Vibrio vulnificus in Seawater and Oysters. Appl Environ Microb. 2012;78(20):7455-66.
Williams HN, Lymperopoulou DS, Athar R, Chauhan A, Dickerson TL, Chen H, et al. Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality. ISME J. 2016;10(2):491-9.
Chen H, Laws EA, Martin JL, Berhane TK, Gulig PA, Williams HN. Relative Contributions of Halobacteriovorax and Bacteriophage to Bacterial Cell Death under Various Environmental Conditions. Mbio. 2018;9(4): e01202-18.
Perez J, Moraleda-Munoz A, Marcos-Torres FJ, Munoz-Dorado J. Bacterial predation: 75 years and counting! Environ Microbiol. 2016;18(3):766-79.
Cabrera G, Perez R, Gomez JM, Abalos A, Cantero D. Toxic effects of dissolved heavy metals on Desulfovibrio vulgaris and Desulfovibrio sp. strains. J Hazard Mater. 2006;135(1-3):40-6.
Im H, Dwidar M, Mitchell RJ. Bdellovibrio bacteriovorus HD100, a predator of Gram-negative bacteria, benefits energetically from Staphylococcus aureus biofilms without predation. Isme J. 2018;12(8):2090-5.
Sockett RE. Predatory Lifestyle of Bdellovibrio bacteriovorus. Annu Rev Microbiol. 2009;63:523-39.
Hespell RB, Thomashow MF, Rittenberg SC. Changes in Cell Composition and Viability of Bdellovibrio bacteriovorus during Starvation. Arch Microbiol. 1974;97(4):313-27.
Pasternak Z, Pietrokovski S, Rotem O, Gophna U, Lurie-Weinberger MN, Jurkevitch E. By their genes ye shall know them: genomic signatures of predatory bacteria. Isme J. 2013;7(4):756-69.
Reiner AM, Shilo M. Host-Independent Growth of Bdellovibrio bacteriovorus in Microbial Extracts. J Gen Microbiol. 1969;59:401-410.
Hobley L, Lerner TR, Williams LE, Lambert C, Till R, Milner DS, et al. Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria. BMC Genomics. 2012;13:670.
Wang ZJ, Liu QQ, Zhao LH, Du ZJ, Chen GJ. Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov. Int J Syst Evol Microbiol. 2015;65(5):1542-9.
Wang S, Mu DS, Zheng WS, Du ZJ. Complete genome sequence of Bradymonas sediminis FA350^T, the first representative of the order Bradymonadales. Marine Genomics. 2019;46(4):62-5.
Hahn MW, Schmidt J, Koll U, Rohde M, Verbarg S, Pitt A, et al. Silvanigrella aquatica gen. nov., sp. nov., isolated from a freshwater lake, description of Silvanigrellaceae fam. nov. and Silvanigrellales ord. nov., reclassification of the order Bdellovibrionales in the class Oligoflexia, reclassification of the families Bacteriovoracaceae and Halobacteriovoraceae in the new order Bacteriovoracales ord. nov., and reclassification of the family Pseudobacteriovoracaceae in the order Oligoflexales. Int J Syst Evol Microbiol. 2017;67(8):2555-68.
Zhou XW, Li SG, Li W, Jiang DM, Han K, Wu ZH, et al. Myxobacterial community is a predominant and highly diverse bacterial group in soil niches. Env Microbiol Rep. 2014;6(1):45-56.
Jiang DM, Kato C, Zhou XW, Wu ZH, Sato T, Li YZ. Phylogeographic separation of marine and soil myxobacteria at high levels of classification. Isme Journal. 2010;4(12):1520-30.
Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ, Chen GJ, et al. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome. 2018;6(1):230.
Guo LY, Li CM, Wang S, Mu DS, Du ZJ. Lujinxingia litoralis gen. nov., sp. nov. and Lujinxingia sediminis sp. nov., two new representatives in the order Bradymonadales. Int J Syst Evol Microbiol. 2019; doi: 10.1099/ijsem.0.003556.
Kim M, Kang O, Zhang Y, Ren L, Chang X, Jiang F, et al. Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii. Int J Syst Evol Microbiol. 2016;66(1):91-100.
Vavourakis CD, Andrei AS, Mehrshad M, Ghai R, Sorokin DY, Muyzer G. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. Microbiome. 2018;6(1):168.
Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9(1):5114.
Gil R, Silva FJ, Pereto J, Moya A. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev. 2004;68(3):518-37.
Avidan O, Petrenko M, Becker R, Beck S, Linscheid M, Pietrokovski S, et al. Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators. Sci Rep. 2017;7(1):1013.
Duncan MC, Gillette RK, Maglasang MA, Corn EA, Tai AK, Lazinski DW, et al. High-Throughput Analysis of Gene Function in the Bacterial Predator Bdellovibrio bacteriovorus. MBio. 2019;10(3): e01040-19.
Dietsche T, Tesfazgi Mebrhatu M, Brunner MJ, Abrusci P, Yan J, Franz-Wachtel M, et al. Structural and Functional Characterization of the Bacterial Type III Secretion Export Apparatus. PLoS Pathog. 2016;12(12):e1006071.
Li J, Chen G, Wu H, Webster JM. Identification of two pigments and a hydroxystilbene antibiotic from Photorhabdus luminescens. Appl Environ Microbiol. 1995;61(12):4329-33.
Nevermann J, Silva A, Otero C, Oyarzun DP, Barrera B, Gil F, et al. Identification of Genes Involved in Biogenesis of Outer Membrane Vesicles (OMVs) in Salmonella enterica Serovar Typhi. Front Microbiol. 2019;10:104.
Liu C, Liu Y, Xu XX, Wu H, Xie HG, Chen L, et al. Potential effect of matrix stiffness on the enrichment of tumor initiating cells under three-dimensional culture conditions. Exp Cell Res. 2015;330(1):123-34.
Grote J, Schott T, Bruckner CG, Glockner FO, Jost G, Teeling H, et al. Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci U S A. 2012;109(2):506-10.
Fukui T, Shiomi N, Doi Y. Expression and characterization of (R)-specific enoyl coenzyme A hydratase involved in polyhydroxyalkanoate biosynthesis by Aeromonas caviae. Journal of Bacteriology. 1998;180(3):667-73.
Sukovich DJ, Seffernick JL, Richman JE, Hunt KA, Gralnick JA, Wackett LP. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Appl Environ Microbiol. 2010;76(12):3842-9.
Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, et al. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004;303(5658):689-92.
Munoz-Dorado J, Marcos-Torres FJ, Garcia-Bravo E, Moraleda-Munoz A, Perez J. Myxobacteria: Moving, Killing, Feeding, and Surviving Together. Front Microbiol. 2016;7:781.
Welsh RM, Zaneveld JR, Rosales SM, Payet JP, Burkepile DE, Thurber RV. Bacterial predation in a marine host-associated microbiome. Isme J. 2016;10(6):1540-4.
Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. New insights from uncultivated genomes of the global human gut microbiome. Nature. 2019;568(7753):505-510.
Black PN, DiRusso CC. Transmembrane movement of exogenous long-chain fatty acids: proteins, enzymes, and vectorial esterification. Microbiol Mol Biol Rev. 2003;67(3):454-72.
Morris JJ, Lenski RE, Zinser ER. The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss. Mbio. 2012;3(2):00036-12.
Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, et al. Massive gene decay in the leprosy bacillus. Nature. 2001;409(6823):1007-11.
Saunders AM, Mabbett AN, McEwan AG, Blackall LL. Proton motive force generation from stored polymers for the uptake of acetate under anaerobic conditions. FEMS Microbiol Lett. 2007;274(2):245-51.
Kim KS, Rao NN, Fraley CD, Kornberg A. Inorganic polyphosphate is essential for long-term survival and virulence factors in Shigella and Salmonella spp. P Natl Acad Sci USA. 2002;99(11):7675-80.
Ratcliff WC, Kadam SV, Denison RF. Poly-3-hydroxybutyrate (PHB) supports survival and reproduction in starving rhizobia. FEMS Microbiol Ecol. 2008;65(3):391-9.
Moller L, Laas P, Rogge A, Goetz F, Bahlo R, Leipe T, et al. Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: possible implications for their ecology. Isme J. 2019;13(2):482-93x.
Kuroda A, Nomura K, Ohtomo R, Kato J, Ikeda T, Takiguchi N, et al. Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli. Science. 2001;293(5530):705-8.
Granato ET, Meiller-Legrand TA, Foster KR. The Evolution and Ecology of Bacterial Warfare. Curr Biol. 2019;29(11):R521-R37.
Chamot-Rooke J, Mikaty G, Malosse C, Soyer M, Dumont A, Gault J, et al. Posttranslational Modification of Pili upon Cell Contact Triggers N. meningitidis Dissemination. Science. 2011;331(6018):778-82.
Ellison CK, Dalia TN, Ceballos AV, Wang JCY, Biais N, Brun YV, et al. Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae. Nat Microbiol. 2018;3(7):773-780.
Craig L, Forest KT, Maier B. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol. 2019;17(7):429-40.
Ruhe ZC, Subramanian P, Song KH, Nguyen JY, Stevens TA, Low DA, et al. Programmed Secretion Arrest and Receptor-Triggered Toxin Export during Antibacterial Contact-Dependent Growth Inhibition. Cell. 2018;175(4):921-933.
Fernandez-Gomez B, Richter M, Schuler M, Pinhassi J, Acinas SG, Gonzalez JM, et al. Ecology of marine Bacteroidetes: a comparative genomics approach. Isme J. 2013;7(5):1026-37.
Mu D, Zhao J, Wang Z, Chen G, Du Z. Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China. Genome Announc. 2016;4(1):e01555-15.
Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou JZ, et al. A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights. Journal of Bacteriology. 2014;196(12):2210-5.
Mu DS, Yu XX, Xu ZX, Du ZJ, Chen GJ. Physiological and transcriptomic analyses reveal mechanistic insight into the adaption of marine Bacillus subtilis C01 to alumina nanoparticles. Sci Rep. 2016;6:srep29953.
Westermann AJ, Forstner KU, Amman F, Barquist L, Chao Y, Schulte LN, et al. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions. Nature. 2016;529(7587):496-501.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research. 2014;42(D1):D206-D14.
Ellison CK, Kan J, Dillard RS, Kysela DT, Ducret A, Berne C, et al. Obstruction of pilus retraction stimulates bacterial surface sensing. Science. 2017;358(6362):535-8.
Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. Peerj. 2016;4:2584.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312-3.
Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490.
Liu XB, Li M, Castelle CJ, Probst AI, Zhou ZC, Pan J, et al. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. Microbiome. 2018;6:102.
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol. 2018;56(4):280-5.
Yu GC, Smith DK, Zhu HC, Guan Y, Lam TTY. GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8(1):28-36.

Table 1. The features of 3 different types of bacterial predators

Current predator type	Redefined predator type	Metabolic pathway deficiencies	Pure-culture cultivable	Storing nutrients as polymers	Predation strategy	Predation specificity
Obligate	Highly prey-dependent	High	Extremely difficult	None	Contact-dependent	Gram-negative
Bradymonabacteria	Facultatively prey-dependent	High	Difficult	Polyhydroxyalkanoates, polyphosphate, and alkanes	Contact-dependent	Gram-negative and Gram-positive
Facultative	Prey-independent	Low	Normal	Polyphosphate*	Mostly contact-independent	Gram-negative and Gram-positive

* A polyphosphate accumulation pathway was found in genomes but not determined by experiments.

Download PDF

Journal Publication

published 31 Aug, 2020

Read the published version in Microbiome →

Editorial decision: Minor revision
22 Jun, 2020
Review #3 received at journal
16 Jun, 2020
Review #2 received at journal
16 Jun, 2020
Reviewer #3 agreed at journal
26 May, 2020
Review #1 received at journal
20 Apr, 2020
Reviewer #2 agreed at journal
16 Apr, 2020
Reviewer #1 agreed at journal
29 Mar, 2020
Reviewers invited by journal
26 Mar, 2020
Editor assigned by journal
05 Mar, 2020
Submission checks completed at journal
04 Mar, 2020
Editor invited by journal
04 Mar, 2020

You are reading this older preprint version

Read the latest preprint version →

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

Status:

Journal Publication

Version 2

Abstract

Figures

Background

Results

Discussion

Conclusion

Methods

Declarations

References

Table 1

Supplementary Files

Status:

Journal Publication

Version 2