The Sinorhizobium meliloti LpxXL and AcpXL Proteins Play Important Roles in Bacteroid Development within Alfalfa

Free-living Sinorhizobium meliloti lpxXL and acpXL mutants lack lipid A very-long-chain fatty acids (VLCFAs) and have reduced competitiveness in alfalfa. We demonstrate that LpxXL and AcpXL play important but distinct roles in bacteroid development and that LpxXL is essential for the modification of S. meliloti bacteroid lipid A with VLCFAs.Sinorhizobium meliloti and Brucella abortus form chronic intracellular infections within legumes and mammalian hosts, respectively (3, 20), and their BacA proteins play essential roles in these processes (8, 12). The precise function(s) of the BacA proteins has not been resolved, but free-living S. meliloti and B. abortus mutants lacking BacA have increased resistance to the glycopeptide bleomycin (9, 12) and there are ∼50% decreases in their lipid A very-long-chain fatty acid (VLCFA) contents (4, 7). It has also been determined that the increased resistance of an S. meliloti bacA null mutant to bleomycin and a truncated eukaryotic peptide, Bac7_1-16, is independent of its lipid A VLCFA alteration (6, 15). Together, these findings support a model in which BacA could have multiple nonoverlapping functions which lead to lipid A VLCFA modification and peptide uptake. The fact that two symbiotically defective S. meliloti BacA site-directed mutants (Q193G and R389G) (13) show defects in BacA-mediated lipid A VLCFA modification (4) but are still capable of peptide uptake (15) suggests that the S. meliloti lipid A VLCFA modification could play a key role in the symbiosis of this organism with alfalfa.Since the mechanism by which BacA leads to the lipid A VLCFA modification has not been resolved (4), S. meliloti mutants were constructed with mutations in the lpxXL and acpXL genes, which encode a lipid A VLCFA acyl transferase and a VLCFA acyl carrier protein directly involved in the biosynthesis of VLCFA-modified lipid A (5, 23). The S. meliloti lpxXL and acpXL mutants completely lack the lipid A VLCFA modification in their free-living states, but, unlike the S. meliloti bacA null mutant, these mutants can still form a successful symbiosis with alfalfa (5, 8, 23). However, the fact that the S. meliloti acpXL and lpxXL mutants are substantially less competitive in the alfalfa symbiosis than the parent strain (5, 23) indicates that the AcpXL and LpxXL proteins play important roles in at least one of the stages of the alfalfa symbiosis. Although the free-living S. meliloti acpXL and lpxXL mutants completely lack the lipid A VLCFA, they produce different species of lipid A (5). For example, in the absence of AcpXL, S. meliloti is able to modify lipid A with either C16:0 or C18:0 in the position normally modified with the VLCFA in the parent strain lipid A. This process is LpxXL dependent, as it does not occur in either an S. meliloti lpxXL single mutant or an S. meliloti acpXL lpxXL double mutant. In addition, since a Rhizobium leguminosarum acpXL mutant completely lacks the lipid A VLCFA modification in its free-living state but its lipid A is partially modified with the VLCFA to ∼58% of the amount in the parent strain lipid A during passage through peas (25), it is also possible that the S. meliloti acpXL mutant and possibly the S. meliloti lpxXL mutant undergo further lipid A changes during the interaction with alfalfa.In this study, we found that LpxXL and AcpXL play important but distinct roles in S. meliloti bacteroid development during alfalfa symbiosis. Additionally, we demonstrated that there is a minor host-induced AcpXL-independent mechanism by which S. meliloti bacteroid lipopolysaccharide (LPS) can be modified with the VLCFA. In contrast, we found that the LpxXL protein plays an essential role in the modification of S. meliloti bacteroids with VLCFAs.     

The Twin Arginine Transport System Appears To Be Essential for Viability in Sinorhizobium meliloti

The twin arginine transport (Tat) system is responsible for transporting prefolded proteins to the periplasmic space. The Tat pathway has been implicated in many bacterial cellular functions, including motility, biofilm formation, and pathogenesis and symbiosis. Since the annotation of Sinorhizobium meliloti Rm1021 genome suggests that there may be up to 94 putative Tat substrates, we hypothesized that characterizing the twin arginine transport system in this organism might yield unique data that could help in the understanding of twin arginine transport. To initiate this work we attempted a targeted mutagenesis of the tat locus. Despite repeated attempts using a number of different types of media, the attempts at mutation construction were unsuccessful unless the experiment was carried out in a strain that was merodiploid for tatABC. In addition, it was shown that a plasmid carrying tatABC was stable in the absence of antibiotic selection in a tat deletion background. Finally, fluorescence microscopy and live/dead assays of these cultures show a high proportion of dead and irregularly shaped cells, suggesting that the loss of tatABC is inversely correlated with viability. Taken together, the results of this work provide evidence that the twin arginine transport system of S. meliloti appears to be essential for viability under all the conditions that we had tested.Sinorhizobium meliloti is a Gram-negative alphaproteobacterium capable of entering into a symbiotic relationship with leguminous plants such as alfalfa. Within the rhizosphere, rhizobia are capable of sensing flavones or isoflavones secreted by the host plant (4, 46, 57). In response, a cascade of events ensues that leads to the eventual attachment of the bacteria to the plant root, infection thread development, and finally release of the bacteria within the differentiated plant cells of the developing nodule structure (34, 45). It is within this tightly regulated environment that the rhizobia express the genes that encode the proteins required for nitrogen fixation and that result in the reduction of atmospheric N₂ to NH_4. In exchange for the production of nitrogen, the plant provides nutrients for the bacteria to grow and to establish the symbiotic relationship (33, 50).Protein targeting and translocation are important processes for correct cellular function within all living organisms. It is predicted in Escherichia coli that more than 450 proteins are transported across the cytoplasmic membrane (43). The vast majority of these proteins are transported through the general secretory (Sec) system, with a minority being transported by the more recently discovered twin arginine transport (Tat) pathway (43). Proteins that are targeted to the cytoplasmic membrane in Gram-negative bacteria via the Sec system rely on a core set of proteins that include SecA, a protein that has ATPase function, SecYEG, which define the minimum membrane transport apparatus, and in some cases a chaperone protein, SecB (18, 54). The translated protein is carried toward the membrane with help from the chaperone SecB and relayed to the SecYEG apparatus that threads the proteins through the membrane in a linear fashion, with the energy for transport being derived from the hydrolysis of ATP, which is provided by SecA (18).In contrast, the Tat system is believed to transport proteins that have already undergone folding and, in many cases, cofactor insertion (41, 60). In brief, following protein translation, a chaperone may be involved to help transfer the substrate to the TatBC complex, where the TatC component recognizes the twin arginine signal motif, (S/T)RRXFLK (1, 42). The TatBC complex subsequently recruits TatA oligomers that coordinately make up the membrane pore required for transport (8, 29, 31). Using the pH gradient (ΔpH), the Tat substrate protein is transported through the TatA pore in its folded state and integrated into the membrane or transported further to the periplasmic space (3, 39).Approximately 30 proteins are predicted to be transported through the Tat system in E. coli (43). The majority of these appear to be expressed or function anaerobically (43). Interestingly, bioinformatic analysis of S. meliloti and Rhizobium leguminosarum suggests that a much larger number of proteins may use the Tat system in these organisms (36). In addition, these organisms are classified as obligate aerobic organisms (12, 28, 55).Since tat mutations have been shown to affect many bacteria-host interactions (17, 25, 36, 49, 62), we set out to construct a tat mutation in S. meliloti to elucidate the role that tat may have in determining the bacteria''s ability to interact with its host plant and affect nodule development. Moreover, we reasoned that a tat mutation in S. meliloti might help characterize putative Tat substrates in a different model organism. Surprisingly, we were able to construct a tat mutation only in a merodiploid strain that contained the tatABC genes on a plasmid in trans. Using plasmid stability, transduction experiments, and live/dead assays, we show that the tat region in S. meliloti appears to be required for viability and is an essential region of the chromosome. This is the first work to show that Tat is required for viability in a bacterial species.     

Cellular Localization of Predicted Transmembrane and Soluble Chemoreceptors in Sinorhizobium meliloti

Bacterial chemoreceptors primarily locate in clusters at the cell pole, where they form large sensory complexes which recruit cytoplasmic components of the signaling pathway. The genome of the soil bacterium Sinorhizobium meliloti encodes seven transmembrane and two soluble chemoreceptors. We have investigated the localization of all nine chemoreceptors in vivo using genome-encoded fusions to a variant of the enhanced green fluorescent protein and to monomeric red fluorescent protein. Six of the transmembrane (McpT to McpX and McpZ) and both soluble (McpY and IcpA) receptors localize to the cell pole. Only McpS, encoded from the symbiotic plasmid pSymA, is evenly distributed in the cell. While the synthesis of all polar localized receptors is confined to exponential growth correlating with the motility phase of cells, McpS is only weakly expressed throughout cell culture growth. Therefore, motile S. meliloti cells form one major chemotaxis cluster that harbors all chemoreceptors except for McpS. Colocalization and deletion analysis demonstrated that formation of polar foci by the majority of receptors is dependent on other chemoreceptors and that receptor clusters are stabilized by the presence of the chemotaxis proteins CheA and CheW. The transmembrane McpV and the soluble IcpA localize to the pole independently of CheA and CheW. However, in mutant strains McpV formed delocalized polar caps that spread throughout the cell membrane while IcpA exhibited increased bipolarity. Immunoblotting of fractionated cells revealed that IcpA, which lacks any hydrophobic domains, nevertheless is associated to the cell membrane.The chemosensory machinery of Escherichia coli and other bacteria is arranged in large protein clusters (22, 28, 43, 49). One individual signaling unit is formed by a ternary assembly of chemoreceptor dimers, the histidine kinase CheA, and the so-called adaptor protein CheW. E. coli cells contain 20,000 receptor molecules (22). Recent studies suggest that the stoichiometry of such chemosensory complexes is flexible (17, 32). Allosteric interactions among receptors in a chemosensory cluster facilitate amplification and integration of chemotactic stimuli (20, 21, 41, 42).In contrast to E. coli, which has a single set of che genes and only five receptors, some species from the alpha subgroup of the proteobacteria, such as Pseudomonas aeruginosa, Rhodobacter sphaeroides, and Sinorhizobium meliloti, encode multiple chemotaxis-like systems, reflecting their complex lifestyle. The opportunistic pathogen P. aeruginosa possesses four chemotaxis systems that together have 26 known receptor genes (47), while the nonsulfur bacterium R. sphaeroides has three separate che operons with 13 known receptor-like genes (27).The symbiotic soil bacterium S. meliloti possesses eight methyl-accepting chemotaxis proteins (MCPs), McpS to McpZ, and one transducer-like-protein, IcpA, which lacks the conserved Glu or Gln residues that serve as methyl-accepting sites (29). Seven of the MCP proteins are localized in the cytoplasmic membrane via two membrane-spanning regions, whereas McpY and IcpA lack such hydrophobic regions. The S. meliloti mcpS gene is the third gene of the che2 operon located on the symbiotic plasmid pSymA (4). The icpA gene is the first gene of the chromosomal che operon comprising a total of 10 genes (9). This operon is part of the flagellar gene cluster with 56 chemotaxis, motor, and flagellar genes residing on one contiguous 51.4-kb chromosomal region (7, 46). For bacteria with numerous chemoreceptor genes, it is not unusual to find most of them located outside chemotaxis operons. This is the case with six monocistronic S. meliloti mcp genes which are scattered throughout the genome. The remaining mcpW gene is cotranscribed with a putative cheW gene. In this study, we examined the localization of the nine receptor gene products in the S. meliloti cell by fluorescence microscopy in wild-type and various deletion strains. The cellular localization of the two soluble receptors, McpY and IcpA, was also analyzed in vitro using an immunoblot assay on fractionated cell components. Furthermore, timing of chemoreceptor gene expression during exponential and stationary phase was determined.     

Sinorhizobium meliloti Mutants Deficient in Phosphatidylserine Decarboxylase Accumulate Phosphatidylserine and Are Strongly Affected during Symbiosis with Alfalfa

Sinorhizobium meliloti contains phosphatidylglycerol, cardiolipin, phosphatidylcholine, and phosphatidylethanolamine (PE) as major membrane lipids. PE is formed in two steps. In the first step, phosphatidylserine synthase (Pss) condenses serine with CDP-diglyceride to form phosphatidylserine (PS), and in the second step, PS is decarboxylated by phosphatidylserine decarboxylase (Psd) to form PE. In this study we identified the sinorhizobial psd gene coding for Psd. A sinorhizobial mutant deficient in psd is unable to form PE but accumulates the anionic phospholipid PS. Properties of PE-deficient mutants lacking either Pss or Psd were compared with those of the S. meliloti wild type. Whereas both PE-deficient mutants grew in a wild-type-like manner on many complex media, they were unable to grow on minimal medium containing high phosphate concentrations. Surprisingly, the psd-deficient mutant could grow on minimal medium containing low concentrations of inorganic phosphate, while the pss-deficient mutant could not. Addition of choline to the minimal medium rescued growth of the pss-deficient mutant, CS111, to some extent but inhibited growth of the psd-deficient mutant, MAV01. When the two distinct PE-deficient mutants were analyzed for their ability to form a nitrogen-fixing root nodule symbiosis with their alfalfa host plant, they behaved strikingly differently. The Pss-deficient mutant, CS111, initiated nodule formation at about the same time point as the wild type but did form about 30% fewer nodules than the wild type. In contrast, the PS-accumulating mutant, MAV01, initiated nodule formation much later than the wild type and formed 90% fewer nodules than the wild type. The few nodules formed by MAV01 seemed to be almost devoid of bacteria and were unable to fix nitrogen. Leaves of alfalfa plants inoculated with the mutant MAV01 were yellowish, indicating that the plants were starved for nitrogen. Therefore, changes in lipid composition, including the accumulation of bacterial PS, prevent the establishment of a nitrogen-fixing root nodule symbiosis.Rhizobia are soil bacteria able to form a symbiosis with legume plants, which leads to the formation of nitrogen-fixing root nodules. The establishment and functioning of this symbiosis are based on the recognition of signal molecules, which are produced by both the bacterial and plant partners. Known recognition factors of the bacterial endosymbiont include nodulation (Nod) factors, extracellular polysaccharides, lipopolysaccharides, K antigens, and cyclic glucans (24, 53). These factors are required for nodule formation, the infection process, and the colonization of the root nodule. Recently it was demonstrated that adequate levels of phosphatidylcholine (PC) are also required in order to allow the formation of a fully functional symbiosis between Bradyrhizobium japonicum and its soybean host plant (35). Under conditions of phosphate limitation, Sinorhizobium meliloti replaces the majority of its phospholipids with phosphorus-free membrane lipids, such as sulfolipids, ornithine-containing lipids, and diacylglyceryl-N,N,N-trimethylhomoserine lipids (20). Rhizobial mutants lacking the ability to form any one of these phosphorus-free membrane lipids or all three lipids at the same time form effective nitrogen-fixing root nodules (30, 31), demonstrating that not all major bacterial membrane lipids are required for the onset of a successful symbiosis.Escherichia coli is the prokaryote with the best-studied membrane lipid biosynthesis. In E. coli, three major membrane phospholipids, phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin (CL), are present. Certain functions have been defined for specific membrane phospholipids in E. coli. Anionic phospholipids (PG and CL) were shown to be involved in the initiation of DNA replication (60) and in the translocation of outer membrane precursor proteins (27). The zwitterionic PE is essential for a proper functioning of the electron transfer chain (34), for the assembly and functionality of lactose permease (4, 5), and for motility and chemotaxis (47). Certain specific functions have also been shown for other membrane lipids. Recently PC has been shown to be required for pathogenesis of Legionella pneumophila, Brucella abortus, and Agrobacterium tumefaciens on their hosts (7, 8, 9, 59). The cationic membrane lipid lysyl-phosphatidylglycerol is involved in conferring resistance to cationic antimicrobial peptides of the host''s innate immune system to Staphylococcus aureus (40), and the presence of LPG in Rhizobium tropici also increases resistance to the cationic peptide polymyxin B (52).In the initial step of the pathway leading to PE formation, phosphatidylserine (PS) synthase (Pss) is responsible for the formation of PS from CDP-diacylglycerol and serine (EC 2.7.8.8) (Fig. ​(Fig.1).1). In the subsequent step, PS is decarboxylated by PS decarboxylase (Psd) (EC 4.1.1.65) to yield PE (17, 58). In S. meliloti, PE is a substrate for the enzyme phospholipid N-methyltransferase (PmtA) (15), leading to the formation of PC. A gene coding for the Pss enzyme (pssA) has been found and cloned from prokaryotes (11, 19, 38, 51), lower eukaryotes, such as Saccharomyces cerevisiae (28, 37), and plants (12). In a previous work we described the construction and characterization of an S. meliloti mutant deficient in Pss (51).Open in a separate windowFIG. 1.Biosynthesis of phospholipids in Sinorhizobium meliloti. SAM, S-adenosylmethionine; SAHC, S-adenosylhomocysteine; PgsA, phosphatidylglycerolphosphate synthase; Pgp, phosphatidylglycerolphosphate phosphatase; Cls, cardiolipin synthase; Pss, phosphatidylserine synthase; Psd, phosphatidylserine decarboxylase; PmtA, phospholipid N-methyltransferase; Pcs, phosphatidylcholine synthase.Psds have been described and characterized for a wide range of organisms, including bacteria, such as E. coli (22, 23, 29) and Bacillus subtilis (32), lower eukaryotes, such as S. cerevisiae (6, 54-56) and Plasmodium falciparum (1), plants, such as Arabidopsis thaliana (36, 41), and mammals (CHO [Chinese hamster ovary] cells) (26). All Psd sequences identified so far seem to be phylogenically related (see Fig. S1A in the supplemental material). Interestingly, S. meliloti lacks a good homologue to any of the above-mentioned Psds.Here we describe the identification and characterization of the sinorhizobial psd gene coding for Psd. The mutant MAV01, in which the sinorhizobial psd gene is deleted, accumulated PS to about 20% of total lipids when grown in complex growth medium. We compared the mutant MAV01 to a sinorhizobial mutant deficient in Pss (CS111) (51) under free-living conditions and during symbiosis. The Pss-deficient mutant, CS111, forms about 30% fewer nodules than the wild type on its alfalfa host plant, whereas the PS-accumulating mutant, MAV01, forms 90% fewer nodules than the wild type. Nodule formation in the mutant MAV01 sets in about 20 days later than that in the wild type. The few nodules formed by the psd-deficient mutant seem to be almost devoid of bacteria and are not able to fix nitrogen. Leaves of alfalfa plants inoculated with the mutant MAV01 are yellowish, indicating that the plants are starved for nitrogen. The accumulation of PS, therefore, although allowing wild-type-like growth in different growth media, strongly interferes with nodule development.     

A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have been shown to be powerful and pragmatic molecular methods for typing large numbers of microbial strains for population genetics studies, delineation of species, and assignment of strains to defined bacterial species (4, 13, 27, 40, 44). To date, MLST/MLSA schemes have been applied only to a few vector-borne microbial populations (1, 6, 30, 37, 40, 41, 47).Lyme borreliosis (LB) spirochetes comprise a diverse group of zoonotic bacteria which are transmitted among vertebrate hosts by ixodid (hard) ticks. The most common agents of human LB are Borrelia burgdorferi (sensu stricto), Borrelia afzelii, Borrelia garinii, Borrelia lusitaniae, and Borrelia spielmanii (7, 8, 12, 35). To date, 15 species have been named within the group of LB spirochetes (6, 31, 32, 37, 38, 41). While several of these LB species have been delineated using whole DNA-DNA hybridization (3, 20, 33), most ecological or epidemiological studies have been using single loci (5, 9-11, 29, 34, 36, 38, 42, 51, 53). Although some of these loci have been convenient for species assignment of strains or to address particular epidemiological questions, they may be unsuitable to resolve evolutionary relationships among LB species, because it is not possible to define any outgroup. For example, both the 5S-23S intergenic spacer (5S-23S IGS) and the gene encoding the outer surface protein A (ospA) are present only in LB spirochete genomes (36, 43). The advantage of using appropriate housekeeping genes of LB group spirochetes is that phylogenetic trees can be rooted with sequences of relapsing fever spirochetes. This renders the data amenable to detailed evolutionary studies of LB spirochetes.LB group spirochetes differ remarkably in their patterns and levels of host association, which are likely to affect their population structures (22, 24, 46, 48). Of the three main Eurasian Borrelia species, B. afzelii is adapted to rodents, whereas B. valaisiana and most strains of B. garinii are maintained by birds (12, 15, 16, 23, 26, 45). However, B. garinii OspA serotype 4 strains in Europe have been shown to be transmitted by rodents (17, 18) and, therefore, constitute a distinct ecotype within B. garinii. These strains have also been associated with high pathogenicity in humans, and their finer-scale geographical distribution seems highly focal (10, 34, 52, 53).In this study, we analyzed the intra- and interspecific phylogenetic relationships of B. burgdorferi, B. afzelii, B. garinii, B. valaisiana, B. lusitaniae, B. bissettii, and B. spielmanii by means of a novel MLSA scheme based on chromosomal housekeeping genes (30, 48).     

Identification of Tail Genes in the Temperate Phage 16-3 of Sinorhizobium meliloti 41

Genes encoding the tail proteins of the temperate phage 16-3 of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti 41 have been identified. First, a new host range gene, designated hII, was localized by using missense mutations. The corresponding protein was shown to be identical to the 85-kDa tail protein by determining its N-terminal sequence. Electron microscopic analysis showed that phage 16-3 possesses an icosahedral head and a long, noncontractile tail characteristic of the Siphoviridae. By using a lysogenic S. meliloti 41 strain, mutants with insertions in the putative tail region of the genome were constructed and virion morphology was examined after induction of the lytic cycle. Insertions in ORF017, ORF018a, ORF020, ORF021, the previously described h gene, and hII resulted in uninfectious head particles lacking tail structures, suggesting that the majority of the genes in this region are essential for tail formation. By using different bacterial mutants, it was also shown that not only the RkpM and RkpY proteins but also the RkpZ protein of the host takes part in the formation of the phage receptor. Results for the host range phage mutants and the receptor mutant bacteria suggest that the HII tail protein interacts with the capsular polysaccharide of the host and that the tail protein encoded by the original h gene recognizes a proteinaceous receptor.The Sinorhizobium meliloti-Medicago symbiosis is an important model for endosymbiotic nitrogen fixation. The genome sequence of S. meliloti (strain 1021) has been established (14), and the Medicago truncatula genome is under intensive investigation (3). Phage 16-3 is a temperate, double-stranded DNA phage of S. meliloti strain 41. It is by far the best-studied rhizobiophage and serves as a tool in analyses of rhizobium genetics, in the isolation of some symbiotic mutants, and in the construction of special vectors. Genetic determinants and molecular mechanisms of many aspects of the 16-3 life cycle, such as phage integration and excision (8, 26, 38), regulation of the lytic/lysogenic switch (5, 6, 9, 24, 28), immunity to superinfection (4), phage DNA packaging (15), and the role of gene h in the host range (32), have been examined in detail. Moreover, the complete 60-kb phage genome sequence (accession no. {"type":"entrez-nucleotide","attrs":{"text":"DQ500118","term_id":"111054886","term_text":"DQ500118"}}DQ500118) has been determined recently (P. P. Papp et al., unpublished results). However, little is known about the genes and structural elements involved in the interaction between the phage and its host, and furthermore, only one study of the 16-3 virion proteins has been reported (11).The initial interaction between a tailed phage and its bacterial host cell is mediated by the distal part of the phage tail, which specifically binds to the phage receptor located on the host surface. Earlier results demonstrated that phage 16-3 adsorption is connected to the strain-specific capsular polysaccharide of S. meliloti 41, the K_R5 antigen. So far, three bacterial gene clusters involved in K_R5 antigen production, including the rkp-1, rkp-2, and rkp-3 regions, have been described. rkp mutants are defective in the invasion of the host plant for symbiosis. In addition, they cannot adsorb phage 16-3, suggesting that the K_R5 antigen is required for both functions (19, 20, 30).In order to elucidate the molecular mechanism of phage 16-3 and S. meliloti 41 recognition, bacterial mutants carrying an altered phage receptor and host range phage mutants able to overcome the adsorption block have been characterized previously (32). It was shown that the RkpM protein, together with other yet uncharacterized elements, is a component of the phage receptor. With the use of rkpM mutants, host range mutations in phage gene h, which probably encodes the tail fiber protein, were identified. Interestingly, some mutations influencing phage-host recognition could not be localized in the rkpM and h genes, indicating that on both sides, additional components are important for bacteriophage-host recognition.The aim of this study was to identify additional genetic determinants involved in S. meliloti 41 and phage 16-3 recognition by characterizing new host range and receptor mutants. Furthermore, by using insertional mutagenesis, we examined a region of the phage chromosome supposed to be responsible for tail formation and identified six new genes essential for phage assembly.     

Cultivation of Fastidious Bacteria by Viability Staining and Micromanipulation in a Soil Substrate Membrane System

Soil substrate membrane systems allow for microcultivation of fastidious soil bacteria as mixed microbial communities. We isolated established microcolonies from these membranes by using fluorescence viability staining and micromanipulation. This approach facilitated the recovery of diverse, novel isolates, including the recalcitrant bacterium Leifsonia xyli, a plant pathogen that has never been isolated outside the host.The majority of bacterial species have never been recovered in the laboratory (1, 14, 19, 24). In the last decade, novel cultivation approaches have successfully been used to recover “unculturables” from a diverse range of divisions (23, 25, 29). Most strategies have targeted marine environments (4, 23, 25, 32), but soil offers the potential for the investigation of vast numbers of undescribed species (20, 29). Rapid advances have been made toward culturing soil bacteria by reformulating and diluting traditional media, extending incubation times, and using alternative gelling agents (8, 21, 29).The soil substrate membrane system (SSMS) is a diffusion chamber approach that uses extracts from the soil of interest as the growth substrate, thereby mimicking the environment under investigation (12). The SSMS enriches for slow-growing oligophiles, a proportion of which are subsequently capable of growing on complex media (23, 25, 27, 30, 32). However, the SSMS results in mixed microbial communities, with the consequent difficulty in isolation of individual microcolonies for further characterization (10).Micromanipulation has been widely used for the isolation of specific cell morphotypes for downstream applications in molecular diagnostics or proteomics (5, 15). This simple technology offers the opportunity to select established microcolonies of a specific morphotype from the SSMS when combined with fluorescence visualization (3, 11). Here, we have combined the SSMS, fluorescence viability staining, and advanced micromanipulation for targeted isolation of viable, microcolony-forming soil bacteria.