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A large subfamily of the type IV secretion systems (T4SSs), termed the conjugation systems, transmit mobile genetic elements (MGEs) among many bacterial species. In the initiating steps of conjugative transfer, DNA transfer and replication (Dtr) proteins assemble at the origin‐of‐transfer (oriT) sequence as the relaxosome, which nicks the DNA strand destined for transfer and couples the nicked substrate with the VirD4‐like substrate receptor. Here, we defined contributions of the Dtr protein TraK, a predicted member of the Ribbon‐Helix‐Helix (RHH) family of DNA‐binding proteins, to transfer of DNA and protein substrates through the pKM101‐encoded T4SS. Using a combination of cross‐linking/affinity pull‐downs and two‐hybrid assays, we determined that TraK self‐associates as a probable tetramer and also forms heteromeric contacts with pKM101‐encoded TraI relaxase, VirD4‐like TraJ receptor, and VirB11‐like and VirB4‐like ATPases, TraG and TraB, respectively. TraK also promotes stable TraJ–TraB complex formation and stimulates binding of TraI with TraB. Finally, TraK is required for or strongly stimulates the transfer of cognate (pKM101, TraI relaxase) and noncognate (RSF1010, MobA relaxase) substrates. We propose that TraK functions not only to nucleate pKM101 relaxosome assembly, but also to activate the TrapKM101 T4SS via interactions with the ATPase energy center positioned at the channel entrance. [ABSTRACT FROM AUTHOR]

The translocation of proteins across membranes is a fundamental cellular function. Bacteria have evolved a striking array of pathways for delivering proteins into or across cytoplasmic membranes and, when present, outer membranes. Translocated proteins can form part of the membrane landscape, reside in the periplasmic space situated between the inner and outer membranes of Gram-negative bacteria, deposit on the cell surface, or be released to the extracellular milieu or injected directly into target cells. One protein translocation system, the general secretory pathway, is conserved in all domains of life. A second, the twin-arginine translocation pathway, is also phylogenetically distributed among most bacteria and plant chloroplasts. While all cell types have evolved additional systems dedicated to the translocation of protein cargoes, the number of such systems in bacteria is now known to exceed nine. These dedicated protein translocation systems, which include the types 1 through 9 secretion systems (T1SSs–T9SSs), the chaperone–usher pathway, and type IV pilus system, are the subject of this review. Most of these systems were originally identified and have been extensively characterized in Gram-negative or diderm (two-membrane) species. It is now known that several of these systems also have been adapted to function in Gram-positive or monoderm (single-membrane) species, and at least one pathway is found only in monoderms. This review briefly summarizes the distinctive mechanistic and structural features of each dedicated pathway, as well as the shared properties, that together account for the broad biological diversity of protein translocation in bacteria. [ABSTRACT FROM AUTHOR]

Both indigenous arbuscular mycorrhizal (AM) fungi and phosphate solubilizing bacteria (PSB) are involved in phosphorus (P) mobilization and turnover in agroecosystems. Understanding the diversity and community structure of AM fungi and PSB is important for potentially optimizing their role in mining P for sustainable agriculture. Yet the characteristics of both AM fungi and PSB in response to P input, in particular the influence of different indigenous microbial communities on plant growth has been little studied. Here, we collected soil samples from the top 20 cm of the profile of a soil receiving three fertilizer P rates, comprising nil, optimal (44 kg P ha −1 ) and excessive (131 kg P ha −1 ) P to evaluate the AM fungal community structure and abundance of relevant PSB groups at three sampling times (June, July and September) using 454 pyrosequencing and quantitative-PCR (q-PCR), respectively. In addition, a pot experiment was conducted to investigate the feedback effects of different fractions of indigenous soil microbes on maize seedling growth. The results showed that overall sampling time had a greater impact than P application rate on the community structure of AM fungi and PSB abundance. At each sampling time the AM fungal communities were significantly affected by the fertilizer P rate. The overall abundance of soil microbes and selected taxa were slightly affected by sampling time but not by fertilizer P. Shoot biomass and P nutrition were significantly affected by the microbial community fraction but not by the fertilizer P rate. Changes in AM fungal communities did not lead to significant differences in maize growth. However, long-term absence of P inputs tended to build up microbial communities which greatly suppressed maize growth. Shoot biomass showed a mean decline of 24.4% when grown in inoculated soil compared to sterilized soil. Our results indicate that current P management has not led to negative influences on soil microbial communities. Evidence highlights the need to understand the interactions between plants and microbiome in mining P in order to make maximum use of the most effective indigenous soil microbes for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Summary: Type IV secretion systems (T4SSs) are versatile multiprotein nanomachines spanning the entire cell envelope in Gram‐negative and Gram‐positive bacteria. They play important roles through the contact‐dependent secretion of effector molecules into eukaryotic hosts and conjugative transfer of mobile DNA elements as well as contact‐independent exchange of DNA with the extracellular milieu. In the last few years, many details on the molecular mechanisms of T4SSs have been elucidated. Exciting structures of T4SS complexes from Escherichia coli plasmids R388 and pKM101, Helicobacter pylori and Legionella pneumophila have been solved. The structure of the F‐pilus was also reported and surprisingly revealed a filament composed of pilin subunits in 1:1 stoichiometry with phospholipid molecules. Many new T4SSs have been identified and characterized, underscoring the structural and functional diversity of this secretion superfamily. Complex regulatory circuits also have been shown to control T4SS machine production in response to host cell physiological status or a quorum of bacterial recipient cells in the vicinity. Here, we summarize recent advances in our knowledge of ‘paradigmatic’ and emerging systems, and further explore how new basic insights are aiding in the design of strategies aimed at suppressing T4SS functions in bacterial infections and spread of antimicrobial resistances. [ABSTRACT FROM AUTHOR]

Abstract: The bacterial type IV secretion systems (T4SSs) translocate DNA and protein substrates to bacterial or eukaryotic target cells generally by a mechanism dependent on direct cell-to-cell contact. The T4SSs encompass two large subfamilies, the conjugation systems and the effector translocators. The conjugation systems mediate interbacterial DNA transfer and are responsible for the rapid dissemination of antibiotic resistance genes and virulence determinants in clinical settings. The effector translocators are used by many Gram-negative bacterial pathogens for delivery of potentially hundreds of virulence proteins to eukaryotic cells for modulation of different physiological processes during infection. Recently, there has been considerable progress in defining the structures of T4SS machine subunits and large machine subassemblies. Additionally, the nature of substrate translocation sequences and the contributions of accessory proteins to substrate docking with the translocation channel have been elucidated. A DNA translocation route through the Agrobacterium tumefaciens VirB/VirD4 system was defined, and both intracellular (DNA ligand, ATP energy) and extracellular (phage binding) signals were shown to activate type IV-dependent translocation. Finally, phylogenetic studies have shed light on the evolution and distribution of T4SSs, and complementary structure-function studies of diverse systems have identified adaptations tailored for novel functions in pathogenic settings. This review summarizes the recent progress in our understanding of the architecture and mechanism of action of these fascinating machines, with emphasis on the ‘archetypal’ A. tumefaciens VirB/VirD4 T4SS and related conjugation systems. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey. [Copyright &y& Elsevier]

The Agrobacterium tumefaciens VirB/VirD4 type IV secretion system is composed of a translocation channel and an extracellular T pilus. Bitopic VirB10, the VirB7 lipoprotein, and VirB9 interact to form a cell envelope-spanning structural scaffold termed the "core complex" that is required for the assembly of both structures. The related pKM101-encoded core complex is composed of 14 copies each of these VirB homologs, and the transmembrane (TM) α helices of VirB10-1ike TraF form a 55-Å-diameter ring at the inner membrane. Here, we report that the VirB10 TM helix possesses two types of putative dimerization motifs, a GxxxA (GA4) motif and two leucine (Leu1, Leu2) zippers. Mutations in the Leul motif disrupted T-pilus biogenesis, but these or other mutations in the GA4 or Leu2 motif did not abolish substrate transfer. Replacement of the VirB10 TM domain with a nondimerizing poly-Leu/Ala TM domain sequence also blocked pilus production but not substrate transfer or formation of immunoprecipitable complexes with the core subunits VirB7 and VirB9 and the substrate receptor VirD4. The VirB10 TM helix formed weak homodimers in Escherichia coli, as determined with the TOXCAT assay, whereas replacement of the VirB10 TM helix with the strongly dimerizing TM helix from glycophorin A blocked T-pilus biogenesis in A. tumefaciens. Our findings support a model in which VirB10's TM helix contributes to the assembly or activity of the translocation channel as a weakly self-interacting membrane anchor but establishes a heteromeric TM-TM helix interaction via its Leu1 motif that is critical for T-pilus biogenesis. [ABSTRACT FROM AUTHOR]

Abstract: Nitrogen (N) is a crucial nutrient that requires careful management in intensive cropping systems because of its diverse beneficial and detrimental effects. Here we propose the concept of theoretical N rate (TNR) to answer the important question of how much fertilizer N should be applied to intensive systems based on the N fluxes due to transformation processes in the soil–crop–environment continuum. We define TNR as the theoretically calculated fertilizer N rate with the quantitative relationships of the core N fluxes among fertilizer N, soil N and crop uptake N in the crop root zone to obtain high target yield, maintain soil N balance and minimize environmental risk. We deduced one basic mathematical expression (Nfert =Nuptake −Nstraw +Nfert3) and two simplified expressions [Nfert =(Nuptake −Nstraw)/(1−Coeff); Nfert ≅Nuptake] for calculating the TNR. These expressions do not need much field experimentation or elaborate soil and plant testing to obtain information on crop N demand and soil N supply, and are simple to implement in farming practice to provide a very cost-effective approach. We consider this scheme to be a useful contribution to rational fertilizer practice, especially in developing countries where other N recommendation systems are usually not available and agricultural extension services are poorly developed or absent. [Copyright &y& Elsevier]

Summary Bacteria communicate with each other through contact-independent and -dependent signalling mechanisms. Sensory perception of both types of signals is needed for conjugative transfer of mobile DNA elements via type IV secretion systems (T4SSs) to bacterial or eukaryotic target cells. While the regulatory circuitries coupling extracellular quorum and environmental signals to transcription of T4SS genes are increasingly understood, it remains fundamentally unknown how a potential recipient cell stimulates donor conjugative DNA transfer upon contact. In this issue, ) report use of the male-specific bacteriophage R17, a phage that binds conjugative pili elaborated by IncF plasmid R1, to define requirements for phage-contact-mediated T4SS activation and phage penetration. They report that R17 penetrates only through T4SS channels engaged for delivery of their plasmid cargo to recipient cells. Engagement requires docking of catalytically active relaxase TraI bound at oriT with the TraD substrate receptor (also termed the T4CP). The data, together with recent ultrastructural and biochemical findings, support an intriguing new model that the T4CP cumulatively senses an intracellular signal (substrate docking) and an extracellular signal (pilus bound by phage or a recipient cell) to co-ordinate a late stage morphogenetic or gating reaction that enables bidirectional transmission of nucleoprotein substrates through the T4SS. [ABSTRACT FROM AUTHOR]

Agrobacterium VirB2 pilin is required for assembly of the VirB/VirD4 type IV secretion system (T4SS). The propilin is processed by signal sequence cleavage and covalent linkage of the N and C termini, and the cyclized pilin integrates into the inner membrane (IM) as a pool for assembly of the secretion channel and T pilus. Here, by use of the substituted cysteine accessibility method (SCAM), we defined the VirB2 IM topology and then identified distinct contributions of the T4SS ATPase subunits to the pilin structural organization. Labeling patterns of Cys-substituted pilins exposed to the membrane-impermeative, thiol-reactive reagent 3-(N-maleimidopropionyl) biocytin (MPB) supported a topology model in which two hydrophobic stretches comprise transmembrane domains, an intervening hydrophilic loop (residues 90 to 94) is cytoplasmic, and the hydrophilic N and C termini joined at residues 48 and 121 form a periplasmic loop. Interestingly, the VirB4 ATPase, but not a Walker A nucleoside triphosphate (NTP) binding motif mutant, induced (i) MPB labeling of Cys94, a residue that in the absence of the ATPase is located in the cytoplasmic loop, and (ii) release of pilin from the IM upon osmotic shock. These findings, coupled with evidence for VirB2-VirB4 complex formation by coimmunoprecipitation, support a model in which VirB4 functions as a dislocation motor to extract pilins from the IM during T4SS biogenesis. The VirB11 ATPase functioned together with VirB4 to induce a structural change in the pilin that was detectable by MPB labeling, suggestive of a role for VirB11 as a modulator of VirB4 dislocase activity. [ABSTRACT FROM AUTHOR]

Abstract: Greenhouse field experiments on tomato were carried out at Shouguang, Shandong province, over four double cropping seasons between 2004 and 2008 in order to understand the effects of manipulating root zone N management (RN) on fruit yields, N savings and N losses under conventional furrow irrigation. About 72% of the chemical N fertilizer used in conventional treatment (CN) inputs could be saved using the RN treatment without loss of yield. The cumulative fruit yields were significantly higher in the RN treatment than in the CN treatment. Average seasonal N from irrigation water (118kgNha−1), about 59% of shoot N uptake, was the main nitrogen source in treatments with organic manure application (MN) and without organic manure or nitrogen fertilizer (NN). N losses in the RN treatment were lowered by 54% compared with the CN treatment. Lower N losses were found in the MN and NN treatments due to excessive inputs of organic manure and fruit yields were consequently substantially affected in the NN treatment. The critical threshold of Nmin supply level in the root zone (0–30cm) should be around 150kgNha−1 for sustainable production. April to May in the winter–spring season and September to October in the autumn–winter season are the critical periods for root zone N manipulation during crop growth. However, control of organic manure inputs is another key factor to further reduce surplus N in the future. [Copyright &y& Elsevier]

Type IV secretion systems (T4SS) translocate DNA and protein substrates across prokaryotic cell envelopes generally by a mechanism requiring direct contact with a target cell. Three types of T4SS have been described: (i) conjugation systems, operationally defined as machines that translocate DNA substrates intercellularly by a contact-dependent process; (ii) effector translocator systems, functioning to deliver proteins or other macromolecules to eukaryotic target cells; and (iii) DNA release/uptake systems, which translocate DNA to or from the extracellular milieu. Studies of a few paradigmatic systems, notably the conjugation systems of plasmids F, R388, RP4, and pKM101 and the Agrobacterium tumefaciens VirB/VirD4 system, have supplied important insights into the structure, function, and mechanism of action of type IV secretion machines. Information on these systems is updated, with emphasis on recent exciting structural advances. An underappreciated feature of T4SS, most notably of the conjugation subfamily, is that they are widely distributed among many species of gram-negative and -positive bacteria, wall-less bacteria, and the Archaea. Conjugation-mediated lateral gene transfer has shaped the genomes of most if not all prokaryotes over evolutionary time and also contributed in the short term to the dissemination of antibiotic resistance and other virulence traits among medically important pathogens. How have these machines adapted to function across envelopes of distantly related microorganisms? A survey of T4SS functioning in phylogenetically diverse species highlights the biological complexity of these translocation systems and identifies common mechanistic themes as well as novel adaptations for specialized purposes relating to the modulation of the donor-target cell interaction. [ABSTRACT FROM AUTHOR]

Type IV secretion systems (T4SSs) are versatile secretion systems that are found in both Gram-negative and Gram-positive bacteria and secrete a wide range of substrates, from single proteins to protein–protein and protein–DNA complexes. They usually consist of 12 components that are organized into ATP-powered, double-membrane-spanning complexes. The structures of single soluble components or domains have been solved, but an understanding of how these structures come together has only recently begun to emerge. This Review focuses on the structural advances that have been made over the past 10 years and how the corresponding structural insights have helped to elucidate many of the details of the mechanism of type IV secretion. [ABSTRACT FROM AUTHOR]

Abstract: A split-root experiment investigated the effects of inoculation with the arbuscular mycorrhizal fungus Glomus mosseae and arsenic (As) addition on As uptake by Pteris vittata L. Either part or all of the root system was inoculated with G. mosseae or exposed to As addition (50ml 1000μmolL−1 As 1 week before harvest). Mycorrhizal colonization substantially increased frond and root dry weight and P and As contents irrespective of As addition. Frond As contents in mycorrhizal plants were highest when the whole root system was exposed to As. Frond As concentrations and contents were higher when inoculation and As addition were in the same parts of the root system than when spatially separate. There were positive effects of arbuscular mycorrhiza inoculation on plant growth and As uptake, and inoculation of part of the roots seemed to be as effective as inoculation of the whole root system. [Copyright &y& Elsevier]

Almost all aspects of protein traffic in bacteria were covered at the ASM-FEMS meeting on the topic in Iraklio, Crete in May 2006. The studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. Among the highlights from the meeting that are reviewed here are the molecular dynamics of SecA protein, membrane protein insertion, type III secretion needles and chaperones, type IV secretion, the two partner and autosecretion systems, the ‘secretion competent state’, and the recently discovered type VI secretion system. [ABSTRACT FROM AUTHOR]

Transformation and conjugation permit the passage of DNA through the bacterial membranes and represent dominant modes for the transfer of genetic information between bacterial cells or between bacterial and eukaryotic cells. As such, they are responsible for the spread of fitness-enhancing traits, including antibiotic resistance. Both processes usually involve the recognition of double-stranded DNA, followed by the transfer of single strands. Elaborate molecular machines are responsible for negotiating the passage of macromolecular DNA through the layers of the cell surface. All or nearly all the machine components involved in transformation and conjugation have been identified, and here we present models for their roles in DNA transport. [ABSTRACT FROM AUTHOR]

A glasshouse pot experiment was conducted to investigate the impact of inoculation of cucumber at the germination stage with Glomus etunicatum BEG168 on plant yield and incidence of Fusarium oxysporum f.sp. cucumerinum inoculated 28 days after the start of the experiment. Inoculation with the AM fungus decreased both disease incidence and disease index. Mycorrhizal inoculation also increased P concentrations in the cucumber seedlings. The mycorrhizal seedlings had higher concentrations of proline and polyphenol oxidase activity but lower malondialdehyde than non-mycorrhizal seedlings, indicating that AM inoculation may have protected membrane permeability and reduced the extent of the damage caused by F. oxysporum . The results indicate that the mycorrhizal fungus may influence plant secondary metabolites and increase resistance to wilt disease in cucumber seedlings and may therefore have some potential as a biological control agent. [ABSTRACT FROM AUTHOR]

Type IV secretion (T4S) systems are ancestrally related to bacterial conjugation machines. These systems assemble as a translocation channel, and often also as a surface filament or protein adhesin, at the envelopes of Gram-negative and Gram-positive bacteria. These organelles mediate the transfer of DNA and protein substrates to phylogenetically diverse prokaryotic and eukaryotic target cells. Many basic features of T4S are known, including structures of machine subunits, steps of machine assembly, substrates and substrate recognition mechanisms, and cellular consequences of substrate translocation. A recent advancement also has enabled definition of the translocation route for a DNA substrate through a T4S system of a Gram-negative bacterium. This review emphasizes the dynamics of assembly and function of model conjugation systems and the Agrobacterium tumefaciens VirB/D4 T4S system. We also summarize salient features of the increasingly studied effector translocator systems of mammalian pathogens. [ABSTRACT FROM AUTHOR]

The type IV secretion systems (T4SS) are widely distributed among the Gram-negative and –positive bacteria. These systems mediate the transfer of DNA and protein substrates across the cell envelope to bacterial or eukaryotic cells generally through a process requiring direct cell-to-cell contact. Bacteria have evolved T4SS for survival during establishment of pathogenic or symbiotic relationships with eukaryotic hosts. The Agrobacterium tumefaciens VirB/D4 T4SS and related conjugation machines serve as models for detailed mechanistic studies aimed at elucidating the nature of translocation signals, machine assembly pathways and architectures, and the dynamics of substrate translocation. The A. tumefaciens VirB/D4 T4SS are polar-localized organelles composed of a secretion channel and an extracellular T pilus. These T4SS are assembled from 11 or more subunits. whose membrane topologies, intersubunit contacts and, in some cases, 3-dimensional structures are known. Recently, powerful in vivo assays have identified C-terminal translocation signals, defined for the first time the translocation route for a DNA substrate through a type IV secretion channel, and supplied evidence that ATP energy consumption contributes to a late stage of machine morphogenesis. Together, these recent findings describe the mechanics of type IV secretion in unprecedented detail. [ABSTRACT FROM AUTHOR]

Bacteria use type IV secretion systems (T4SS) to translocate DNA and protein substrates to target cells of phylogenetically diverse taxa. Recently, by use of an assay termed transfer DNA immuno-precipitation (TrIP), we described the translocation route for a DNA substrate (T-DNA, portion of the Ti (tumor-inducing) plasmid that is transferred to plant cells] of the Agrobacterium tumefadens VirB/D4 T4SS in terms of a series of temporally and spatially ordered substrate contacts with subunits of the secretion channel. Here, we report that the bitopic inner membrane protein VirB10 undergoes a structural transition in response to ATP utilization by the VirD4 and VirB11 ATP-binding subunits, as monitored by protease susceptibility. VirB10 interacts with inner membrane VirD4 independently of cellular energetic status, whereas the energy-induced conformational change is required for VirB10 complex formation with an outer membrane-associated heterodimer of VirB7 lipoprotein and VirB9, as shown by coimmunoprecipitation. Under these conditions, the T-DNA substrate is delivered from the inner membrane channel components VirB6 and VirB8 to periplasmic and outer membrane-associated VirB2 pilin and VirB9. We propose that VirD4 and VirB11 coordinate the ATP-dependent formation of a VirB10 "bridge" between inner and outer membrane subassemblies of the VirB/D4 T4SS, and that this morpho- genetic event is required for T-DNA translocation across the A. tumefadens cell envelope. [ABSTRACT FROM AUTHOR]

The translocation of DNA across biological membranes is an essential process for many living organisms. In bacteria, type IV secretion systems (T4SS) are used to deliver DNA as well as protein substrates from donor to target cells. The T4SS are structurally complex machines assembled from a dozen or more membrane proteins in response to environmental signals. In Gram-negative bacteria, the conjugation machines are composed of a cell envelope-spanning secretion channel and an extracellular pilus. These dynamic structures (i) direct formation of stable contacts—the mating junction—between donor and recipient cell membranes, (ii) transmit single-stranded DNA as a nucleoprotein particle, as well as protein substrates, across donor and recipient cell membranes, and (iii) mediate disassembly of the mating junction following substrate transfer. This review summarizes recent progress in our understanding of the mechanistic details of DNA trafficking with a focus on the paradigmatic Agrobacterium tumefaciens VirB/D4 T4SS and related conjugation systems. [Copyright &y& Elsevier]

The increasing number of cases of serogroup C meningococcal disease in Scotland in the late 1990s coincided with the availability of a new meningococcal conjugate serogroup C (MCC) vaccine that, from 1999 onwards, was offered to all individuals aged <20 years. Annual incidence rates between 1994 and 2003 were calculated in 3 age groups (<5 years old; 5-19 years old; and &ges;20 years old), and Poisson regression models were used to verify disease trends over time. Dramatic reductions (P < .05) in the incidence of serogroup C meningococcal disease were seen in target age groups: from 15.8 incidents per 100,000 subjects in 1999 (95% confidence interval [CI], 11.3-20.3) to 0.7 incidents per 100,000 subjects in 2001 (95% CI, -0.3 to 1.6), for subjects <5 years old, and from 6.7 incidents per 100,000 subjects in 1999 (95% CI, 5.1-8.3) to 1.5 incidents per 100,000 subjects in 2001 (95% CI, 0.7-2.3), for subjects 5-19 years old. An increasing incidence of serogroup B meningococcal disease in individuals 5-19 years old was clearly established before the campaign began. A 30% decrease in the case-fatality rate for individuals <20 years old was not significant (P = .1598). The MCC vaccine program has been highly effective in Scotland, leading to substantial reductions in serogroup C meningococcal disease and meningococcal mortality, with no adverse effects on other groups. [ABSTRACT FROM AUTHOR]

Bacteria use conjugation systems, a subfamily of the type IV secretion systems, to transfer DMA to recipient cells. Despite 50 years of research, the architecture and mechanism of action of the channel mediating DNA transfer across the bacterial cell envelope remains obscure. By use of a sensitive, quantifiable assay termed transfer DNA immunoprecipitation (TrIP), we identify contacts between a DNA substrate (T-DNA) and 6 of 12 components of the VirB/D4 conjugation system of the phytopathogen Agrobacterium tumefaciens. Our results define the translocation pathway for a DNA substrate through a bacterial conjugation machine, specifying the contributions of each subunit of the secretory apparatus to substrate passage. [ABSTRACT FROM AUTHOR]

There is increasing and widespread interest in the maintenance of soil quality and remediation strategies for management of soils contaminated with organic pollutants and trace metals or metalloids. There is also a growing body of evidence that arbuscular mycorrhizal (AM) fungi can exert protective effects on host plants under conditions of soil metal contamination. Research has focused on the mechanisms involved and has raised the prospect of utilizing the mutualistic association in soil re-vegetation programmes. In this short paper we briefly review this research, summarize some recent work and highlight some new data which indicate that the alleviation of metal phytotoxicity, particularly Zn toxicity, by arbuscular mycorrhiza may occur by both direct and indirect mechanisms. Binding of metals in mycorrhizal structures and immobilization of metals in the mycorrhizosphere may contribute to the direct effects. Indirect effects may include the mycorrhizal contribution to balanced plant mineral nutrition, especially P nutrition, leading to increased plant growth and enhanced metal tolerance. Further research on the potential application of arbuscular mycorrhiza in the bioremediation or management of metal-contaminated soils is also discussed. [ABSTRACT FROM AUTHOR]

The two-note fee-bee song of male black-capped chickadees functions during the dawn chorus, in part, as a sexual signal across large distances. How song structure might encode information about male quality, however, remains unclear. We studied the availability of cues to male social rank (a proxy indicator of male quality), within the acoustic structure of dawn chorus songs of male chickadees whose flock dominance status we determined the previous winter. We used analysis of variance and discriminant function analysis to demonstrate that five temporal, frequency or relative amplitude features of song can predict individual identity but not the category of social rank (dominant versus subordinate) to which individuals belong. After transmitting chickadee songs through the forest and re-recording them at four broadcast distances, we found that song structure continued to effectively predict singer identity by our statistical methods despite significant acoustic degradation for as long as songs remained audible (up to 80 m). In particular, the relative frequency interval between the two notes is both the most invariant between-male measure and among the most individually distinctive. We conclude the structure of dawn chorus songs could function across large distances to signal the identity of familiar singing males whose relative quality is known to the listener from other interactions (such as encounters within winter flocks). [ABSTRACT FROM AUTHOR]

A record linkage study was done to provide comprehensive data on the epidemiologic characteristics of invasive pneumococcal disease (IPD) in Scotland. The overall incidence of IPD was 11 cases/10[sup5] persons and 21 cases/10[sup5] persons <1 year of age, 51 cases/10[sup5] persons 1 year of age, 45 cases/10[sup5] elderly persons (age ≥65 years), 176–483 cases/10[sup5] persons with chronic medical conditions, and 562–2031 cases/10[sup5] persons with severe immunosuppression. The case-fatality rate was 11% among elderly persons and ranged from 3% to 13% among persons with underlying medical conditions. The most common pneumococcal serogroups associated with IPD were 14, 9, 6, 19, 23, 8, and 4. Serogroups included in the 23-valent polysaccharide vaccine caused the majority of cases of IPD. The proportion of IPD due to the 7­, 9­, and 11­valent conjugate vaccine serogroups was lower among older people and persons with underlying medical conditions. [ABSTRACT FROM AUTHOR]

This study characterized the contribution of the twin-arginine translocation (TAT) pathway to growth, motility, and virulence of the phytopathogen Agrobacterium tumefaciens. In contrast to wild-type strain A348, a tatC null mutant failed to export the green fluorescent protein fused to the trimethylamine N-oxide reductase (TorA) signal sequence or to grow on nitrate as a sole electron acceptor during anaerobic growth. The tatC mutant displayed defects in growth rate and cell division but not in cell viability, and it also released abundant levels of several proteins into the culture supernatant when grown in rich medium or in vir induction minimal medium. Nearly all A348 cells were highly motile in both rich and minimal media. By contrast, approximately 0.1% of the tatC mutant cells were motile in rich medium, and <0.01.% were motile in vir induction medium. Nonmotile tatC mutant cells lacked detectable flagella, whereas motile tatC mutant cells collected from the edge of a motility halo possessed flagella but not because of reversion to a functional TAT system. Motile tatC cells failed to exhibit chemotaxis toward sugars under aerobic conditions or towards nitrate under anaerobic conditions. The tatC mutant was highly attenuated for virulence, only occasionally (∼15% of inoculations) inciting formation of small tumors on plants after a prolonged incubation period of 6 to 8 weeks. However, an enriched subpopulation of motile tatC mutants exhibited enhanced virulence compared to the nonmotile variants. Finally, the tatC mutant transferred T-DNA and protein effectors to plant cells and a mobilizable IncQ plasmid to agrobacterial recipients at wild-type levels. Together, our findings establish that, in addition to its role in secretion of folded cofactor-bound enzymes functioning in alternative respiration, the TAT system of A. tumefaciens is an important virulence determinant. Furthermore, this secretion pathway contributes to flagellar biogenesis and... [ABSTRACT FROM AUTHOR]

We reviewed population-based laboratory reports of invasive meningococcal, pneumococcal, Haemophilus influenzae, Group B Streptococcus (GBS) and Listeria monocytogenes isolates in order to examine the changing epidemiology of meningitis and invasive non-meningitic disease (INMD) caused by these 5 pathogens in the 2 periods before (1983-91) and after (1992-99) routine use of H. influenzae type B conjugate vaccine (Hib) in Scotland. Neissieria meningitidis was the most common cause of meningitis, accounting for 39.2% of cases of meningitis in 1983-91 and 47% of cases in 1992-99, followed by H. influenzae (31%), Streptococcus pneumoniae (22.4%), GBS (3.9%) and L. monocytogenes (3.5%) in 1983-91 and S. pneumoniae (36.3%), H. influenzae (7.8%), GBS (6.1%) and L. monocytogenes (2.8%) in 1992-99. The important epidemiological features of meningitis and INMD caused by these 5 pathogens between 1983-91 and 1992-99 include: 1. The incidence of bacterial meningitis due to S. pneumoniae and GBS was stable; 2. S. pneumoniae was the predominant cause of INMD in both periods; 3. The incidences of INMD caused by N. meningitidis, GBS and S. pneumoniae increased, by 27%, 55% and 56%, respectively; 4. Decreases in the incidences of bacterial meningitis (by 50%) and INMD (by 50%) due to L. monocytogenes were detected; and 5. There were dramatic reductions in the proportions of bacterial meningitis (by 92%) and INMD (by 56%) due to H. influenzae in vaccinated and non-vaccinated individuals. Continued surveillance is necessary to monitor the disease trend, population at risk, serotype distribution and antimicrobial susceptibility in order to implement appropriate public health interventions against invasive bacterial disease. [ABSTRACT FROM AUTHOR]

Examines the intercellular transfer of macromolecule by ancestrally related to conjugation machines. Impact of bacterial conjugation systems to human health; Evolution of secretion pathways; Consideration of bacterial conjugation pathways as type IV secretion family.

Studies the mutagenesis of the Agrobacterium VirE2 single-stranded DNA-binding protein. VirE2 complex formation in Saccharomyces cerevisiae and Agrobacterium tumefaciens; Identification of regions in VirE2 required for homomultimer formation; Localization of domain required for VirE1 interaction.

Provides information on a study to gain genetic evidence for interactions between Agrobacterium tumefaciens VirB11 and other subunits of a transport system. Materials and methodology used to conduct the study; Results of the study; Discussion on the results of the study.

Investigates the transport system responsible for the delivery of oncogenic DNA across the bacterial envelope of the Agrobacterium tumefaciens. Identification of three similarities among conjugation and protein transport processes; Benefits from the early studies of the Escherichia coli F-plasmid system; Overview of the infection process.

Evaluates the membrane topology of VirB4 with the use of the nested deletion method. Description of the method; Information on results; What the resutls indicated; How VirB4 reacted with use of the nested deletion method.

Elucidates the structural, functional and energetic features of the T-complex transport system of Agrobacterium tumefaciens. Immunoblot studies of deltavirB mutants; Virulence; Genetic complementation.

The texture of the soil profile determines the movement and distribution of soil water and also affects plant growth and development. Most studies have focused on the movement of water in homogeneous or layered soil profiles such as coarse sand or gravel as a capillary barrier. Few studies have used loess as an interlayer of sand to study the water distribution characteristics of soil profiles. Here, a layered sand-loess-sand soil profile was constructed in indoor soil columns to explore the effects of different thicknesses of loess interlayer (0, 10 and 20 cm) on water transport. The advancing height of the sand wetting front followed a power function with time in different loess interlayer thickness treatments and the loess interlayer promoted the advancing height of the wetting front. Loess interlayer treatment significantly increased the soil volumetric water content in the corresponding treatment layer (40-60 cm). The thicker the loess interlayer the higher the soil volumetric water content. After two months of soil drainage the volumetric water content in the treatment layer (40-60 cm) corresponding to the loess interlayer treatment did not decline but the control declined by 1.36%. These results may provide a scientific basis and theoretical support for the artificial reconstruction of soil profiles in arid and semi-arid coal mining areas to optimize sand moisture content. [ABSTRACT FROM AUTHOR]

The article offers significant information related to DNA transfer across membranes which is considered to be a fundamental life process. It states that the structure of part of a protein channel that performs this task offers insight into the mechanism of DNA passage through bacterial cell envelopes. It discusses the process called conjugation where many bacterial species transfer DNA to neighbouring cells. It adds that conjugation has played a dominant part in shaping bacterial genomes and poses an enormous public-health problem as a mechanism underlying the rapid dissemination of antibiotic-resistance genes and other virulence traits among pathogens.

Bacterial type IV secretion systems (T4SSs) are a versatile family of macromolecular translocators, collectively able to recruit diverse DNA and protein substrates and deliver them to a wide range of cell types. Presently, there is little understanding of how T4SSs recognize substrate repertoires and form productive contacts with specific target cells. Although T4SSs are composed of a number of conserved subunits and adopt certain conserved structural features, they also display considerable compositional and structural diversity. Here, we explored the structural bases underlying the functional versatility of T4SSs through systematic deletion and subunit swapping between two conjugation systems encoded by the distantly-related IncF plasmids, pED208 and F. We identified several regions of intrinsic flexibility among the encoded T4SSs, as evidenced by partial or complete functionality of chimeric machines. Swapping of VirD4-like TraD type IV coupling proteins (T4CPs) yielded functional chimeras, indicative of relaxed specificity at the substrate—TraD and TraD—T4SS interfaces. Through mutational analyses, we further delineated domains of the TraD T4CPs contributing to recruitment of cognate vs heterologous DNA substrates. Remarkably, swaps of components comprising the outer membrane core complexes, a few F-specific subunits, or the TraA pilins supported DNA transfer in the absence of detectable pilus production. Among sequenced enterobacterial species in the NCBI database, we identified many strains that harbor two or more F-like plasmids and many F plasmids lacking one or more T4SS components required for self-transfer. We confirmed that host cells carrying co-resident, non-selftransmissible variants of pED208 and F elaborate chimeric T4SSs, as evidenced by transmission of both plasmids. We propose that T4SS plasticity enables the facile assembly of functional chimeras, and this intrinsic flexibility at the structural level can account for functional diversification of this superfamily over evolutionary time and, on a more immediate time-scale, to proliferation of transfer-defective MGEs in nature. Author summary: Mobile genetic elements (MGEs) comprise a diverse group of extrachromosomal plasmids or integrated DNA fragments that are widely distributed among many bacterial species. MGEs typically encode conjugation systems dedicated to their transmission to other bacteria, and also code for resistance to antibiotics or virulence or other fitness traits. The conjugation systems, along with an equally medically important group of translocators devoted to the interkingdom delivery of protein effectors by pathogenic species, comprise the superfamily of type IV secretion systems (T4SSs). Recent studies have defined many mechanistic and structural features of the T4SSs, yet there remains little understanding of how T4SSs recruit specific DNA or protein substrates, elaborate functional channels, and in some cases build attachment organelles termed conjugative pili. We explored the mechanics of T4SS machine function by systematically exchanging individual components between two distinct conjugation systems functioning in enterobacterial species. Through construction of chimeric machines, and further mutational analyses, we identified subunits or protein domains of conjugation machines specifying recruitment of different DNA substrates or selectively contributing to assembly of translocation channels or conjugative pili. Such features of T4SSs are prime targets for development of inhibitory strategies aimed at blocking T4SS functions for therapeutic intervention. [ABSTRACT FROM AUTHOR]

Dark septate endophytes (DSE) are widespread colonizers of plant roots and have important ecological functions such as the regulation of plant growth and nutrient uptake. The mechanisms by which DSE mycelium and its extracellular metabolites promote plant growth have not yet been determined. Here, the growth‐promoting effects of DSE mycelium (H) and extracellular metabolites (M) on alfalfa (Medicago sativa L.) were investigated. Treatments H, M and HM increased the total biomass of alfalfa by 23.9%, 47.2% and 47.1%, respectively. H and M modified root structure by increasing root volume and reducing root tissue density, and promoting nutrient uptake. Metabolomic analysis indicates that alfalfa root exudates contained 204 metabolites of different types, mainly lipids and lipid‐like molecules, organic acids and derivatives, benzenoids. There were more organoheterocyclic compounds and fewer organic acids and derivatives in root exudates in treatment H than in treatment M. Pathway analysis shows that DSE and its extracellular metabolites had greater effects on glycerophospholipid metabolism and N‐glycan biosynthesis pathway. The results provide information on the mechanisms involved in the metabolic regulation of plant growth promotion by DSE. [ABSTRACT FROM AUTHOR]

Tidal wetlands sequester vast amounts of organic carbon (OC) and enhance soil accretion. The conservation and restoration of these ecosystems is becoming increasingly geared toward "blue" carbon sequestration while obtaining additional benefits, such as buffering sea‐level rise and enhancing biodiversity. However, the assessments of blue carbon sequestration focus primarily on bulk SOC inventories and often neglect OC fractions and their drivers; this limits our understanding of the mechanisms controlling OC storage and opportunities to enhance blue carbon sinks. Here, we determined mineral‐associated and particulate organic matter (MAOM and POM, respectively) in 99 surface soils and 40 soil cores collected from Chinese mangrove and saltmarsh habitats across a broad range of climates and accretion rates and showed how previously unrecognized mechanisms of climate and mineral accretion regulated MAOM and POM accumulation in tidal wetlands. MAOM concentrations (8.0 ± 5.7 g C kg−1) (±standard deviation) were significantly higher than POM concentrations (4.2 ± 5.7 g C kg−1) across the different soil depths and habitats. MAOM contributed over 51.6 ± 24.9% and 78.9 ± 19.0% to OC in mangrove and saltmarsh soils, respectively; both exhibited lower autochthonous contributions but higher contributions from terrestrial or marine sources than POM, which was derived primarily from autochthonous sources. Increased input of plant‐derived organic matter along the increased temperature and precipitation gradients significantly enriched the POM concentrations. In contrast, the MAOM concentrations depended on climate, which controlled the mineral reactivity and mineral–OC interactions, and on regional sedimentary processes that could redistribute the reactive minerals. Mineral accretion diluted the POM concentrations and potentially enhanced the MAOM concentrations depending on mineral composition and whether the mineral accretion benefited plant productivity. Therefore, management strategies should comprehensively consider regional climate while regulating sediment supply and mineral abundance with engineering solutions to tap the OC sink potential of tidal wetlands. [ABSTRACT FROM AUTHOR]

Summary: Supporting food security while maintaining ecosystem sustainability is one of the most important global challenges for humanity. Optimization of cropping systems is expected to promote the ecosystem services of agroecosystems. Yet, how and why cropping system influences the trade‐offs between economic profitability and multiple ecosystem services remain poorly understood.We investigate the influence of six cropping systems on trade‐offs between economic profitability and multiple ecosystem services after considering 36 agricultural ecosystem properties using field experiment data from 2020 to 2022.We show that designing cropping system is a critical tool to closing the gap between ecosystem sustainability and commercial profitability. Cropping system with three harvests within 2 yr had higher performance in overall ecosystem multiple services through enhancement of supporting, regulating, and economic performance without compromising provisioning compared with four other systems. These systems diminished the trade‐off among multiple services, resulting in a 'win‐win' situation for economics and multiple services. By contrast, the monoculture and double cropping systems lead to a strong trade‐off between pairwise services including ecosystem health and profitability.Our work illustrates the substantial potential of rotation systems with three harvests within 2 yr in enforcing ecosystem services and closing the trade‐offs among multiple agricultural ecosystem services. [ABSTRACT FROM AUTHOR]

[Display omitted] • The proportion and OC content of large aggregates were affected by vegetation types. • The direction of carbon flows was from small aggregates to silt + clay size classes. • Tree plantation slowed carbon flows of aggregates. • Roots are more likely to be the starting point of carbon flow at 15–30cm depth. The vegetation restoration of land post‑mining can promote soil structure development and increase organic carbon storage. The response of soil carbon sequestration pathways to different recovery modes is poorly understood, especially in soils of reclaimed surface-mine areas. Here, long-term carbon dynamics were characterized by examining aggregate-associated carbon contents and carbon flow pathways following vegetation restoration of reclaimed land near a surface mine. Six long-term restoration areas were represented by Populus alba trees, Amorpha fruticosa shrubs, and grassland. During the long-term restoration process the contribution of aggregates to SOC (12.5 to 46.1%), δ13C values (-25.91 to –23.65‰) and percentages of particulate organic carbon in large soil aggregates of tree plantations showed the maximum increase and shrubland showed the minimum. The direction of carbon flows was from small aggregates to silt + clay size classes, and tree plantations slowed the carbon flows of aggregates. With increasing soil depth, roots were more likely to be the starting point of carbon flow in aggregates. This analysis of the natural δ13C signature reveals the mechanism of organic carbon stabilization under long-term vegetation restoration near a surface mine in a semi-arid region. [ABSTRACT FROM AUTHOR]

Bacterial conjugation systems are members of the large type IV secretion system (T4SS) superfamily. Conjugative transfer of F plasmids residing in the Enterobacteriaceae was first reported in the 1940s, yet the architecture of F plasmid-encoded transfer channel and its physical relationship with the F pilus remain unknown. We visualized F-encoded structures in the native bacterial cell envelope by in situ cryoelectron tomography (CryoET). Remarkably, F plasmids encode four distinct structures, not just the translocation channel or channel-pilus complex predicted by prevailing models. The F1 structure is composed of distinct outer and inner membrane complexes and a connecting cylinder that together house the envelopespanning translocation channel. The F2 structure is essentially the F1 complex with the F pilus attached at the outer membrane (OM). Remarkably, the F3 structure consists of the F pilus attached to a thin, cell envelope-spanning stalk, whereas the F4 structure consists of the pilus docked to the OM without an associated periplasmic density. The traffic ATPase TraC is configured as a hexamer of dimers at the cytoplasmic faces of the F1 and F2 structures, where it respectively regulates substrate transfer and F pilus biogenesis. Together, our findings present architectural renderings of the DNA conjugation or "mating" channel, the channel-pilus connection, and unprecedented pilus basal structures. These structural snapshots support a model for biogenesis of the F transfer system and allow for detailed comparisons with other structurally characterized T4SSs. [ABSTRACT FROM AUTHOR]

Indigenous knowledge and approaches to health research have historically been marginalized by Western traditions. Efforts to overcome this marginalization by recognizing Indigenous methodologies as a distinctive form of inquiry are gathering momentum. Health research that seeks to establish levels of agreement about disputed or conceptually unclear subjects frequently relies on consensus methods. Aajiiqatigiingniq is a principle of cultural knowledge and a consensus decision-making approach among Inuit in the Canadian Arctic. We used group meetings and individual interviews involving Inuit elders and other senior community members in Arviat, Nunavut, to explore and describe aajiiqatigiingniq as an appropriate and ethical methodology in qualitative health research. Findings reveal a systematic but apparently informal approach focused on sustained individual and community well-being. Consensus is achieved through the successive addition of group members, respectful communication, mainly narrative discourse, subjective personal engagement, and an unhurried meeting style. While previous research has used Western consensus methods to embed Inuit knowledge in health research, this study provides a first descriptive account of a wholly Inuit consensus methodology. [ABSTRACT FROM AUTHOR]

Biochars and hyperaccumulators have been widely used for the remediation of trace metal contaminated soils through immobilization and phytoextraction. These two options have rarely been used simultaneously despite their potential to achieve a greater decline in trace metal availability and higher removal efficiency in polluted soils. This study investigated the combined effects of biochar and the cadmium/zinc (Cd/Zn) hyperaccumulator Sedum plumbizincicola in a pot experiment and examined the effect of an antibiotic (oxytetracycline, OTC) in an acid soil spiked with Cd/Zn alone and with OTC. Biochar amendment alone significantly decreased soil CaCl 2 -extractable Cd and Zn by 22.7 and 43.1%, respectively. Growing S. plumbizincicola alone resulted in 11.3% Cd and 3.88% Zn removal after ten weeks of phytoextraction. Growing S. plumbizincicola with biochar resulted in higher decreases in extractable Cd and Zn by 60.0% and 53.2%, respectively, and more than three times Cd and Zn removal efficiencies compared to growing S. plumbizincicola without biochar. The results indicate that biochar addition promoted plant growth and increased shoot trace metal concentrations, consequently increasing the removal efficiency and that soil trace metal removal by the hyperaccumulator further reduced the extractable trace metals in addition to immobilization by biochar. Biochar amendment decreased plant OTC concentrations. However, OTC showed no effect on trace metal phytoextraction. Results indicate that the simultaneous use of biochar and the hyperaccumulator can give high Cd/Zn phytoextraction efficiency in terms of both soil total and available trace metal concentrations in acid soils highly contaminated with trace metals or trace metals and OTC. [ABSTRACT FROM AUTHOR]

Background and aims: The addition of organic amendments to soils can significantly increase soil organic matter (SOM) content as well as the mass of large (e.g. 2000-250 μm) particulate organic matter (POM) fractions. Here we address whether the addition of organic amendments might affect both POM pools and the phytoextraction efficiency of Sedum plumbizincicola (S. plumbizincicola) in cadmium (Cd) polluted soils.Methods: We carried out a 442-days long pot experiment and measured Cd uptake by S. plumbizincicola for four successive plant crops in two polluted paddy soils subjected to rice straw (RS) amendment. We also measured soil pH, nutrient availability, pore water dissolved organic carbon (DOC) and Cd concentrations across different soil particle-size fractions.Results: We found that RS amendments had no significant effects on soil pH, DOC or Cd concentrations in bulk soils during repeated phytoextraction. However, RS amendments were associated with significant (1) increases (i.e. 14.3 to 20.7%) in Cd uptake by S. plumbizincicola plants from the first crop harvest, (2) increases in available soil nutrients content, (3) increases in the percentage of oxidizable Cd fractions and the mass of soil POM fractions, and (4) decreases in POM Cd concentrations after repeated phytoextraction. These findings suggest that POM fractions may represent important accessible pools of Cd for uptake by S. plumbizincicola plants.Conclusions: RS amendments enhance both Cd bioavailability within soil POM pools and Cd uptake by the hyperaccumulator S. plumbizincicola thus providing an effective management practice to improve Cd removal from polluted soils through phytoextraction. [ABSTRACT FROM AUTHOR]