Levels Of Relatedness Research Articles

Backyard Farms Represent a Source of Wide Host Range Salmonella Phages That Lysed the Most Common Salmonella Serovars

The genus Salmonella has more than 2,600 serovars, and this trait is important when considering interventions for Salmonella control. Bacteriophages that are used for biocontrol must have an exclusively lytic cycle and the ability to lyse several Salmonella serovars under a wide range of environmental conditions. Salmonella phages were isolated and characterized from 34 backyard production systems (BPSs) with a history of Salmonella infections. BPSs were visited once, and cloacal or fecal samples were processed for phage isolation. Four hosts, Salmonella serovars Enteritidis, Heidelberg, Infantis, and Typhimurium, were used for phage isolation. The host range of the phages was later characterized with a panel of 23 Salmonella serovars (serovar diversity set) and 31 isolates obtained from the same farms (native set). Genetic relatedness for 10 phages with a wide host range was characterized by restriction fragment length polymorphism, and phages clustered based on the host range. We purified 63 phages, and 36 phage isolates were obtained on Salmonella Enteritidis, 16 on Salmonella Heidelberg, and 11 on Salmonella Infantis. Phages were classified in three clusters: (i) phages with a wide host range (cluster I), (ii) phages that lysed the most susceptible Salmonella serovars (serogroup D) and other isolates (cluster II), and (iii) phages that lysed only isolates of serogroup D (cluster III). The most susceptible Salmonella serovars were Enteritidis, Javiana, and Dublin. Seven of 34 farms yielded phages with a wide host range, and these phages had low levels of genetic relatedness. Our study showed an adaptation of the phages in the sampled BPSs to serogroup D Salmonella isolates and indicated that isolation of Salmonella phages with wide host range differs by farm. A better understanding of the factors driving the Salmonella phage host range could be useful when designing risk-based sampling strategies to obtain phages with a wide lytic host range for biocontrol purposes.

Flavisolibacter metallilatus sp. nov., isolated from an automotive air conditioning system and emended description of the genus Flavisolibacter.

A Gram-stain-negative, aerobic, non-motile, rod-shaped and pale yellow-pigmented bacterium, designated strain TX0661T, was isolated from an automotive air conditioning system collected in the Republic of Korea. 16S rRNA gene sequence analysis showed that the strain TX0661T was grouped with members of the genus Flavisolibacter and the strain had 98.2-95.3 % 16S rRNA gene sequence similarities to the species of the genus Flavisolibacter. DNA-DNA relatedness between TX0661T and Flavisolibacter ginsenosidimutans KCTC 22818T and Flavisolibacter ginsengisoli KCTC 12657T was less than 30 %. The low levels of DNA-DNA relatedness identified strain TX0661T as a novel species in the genus Flavisolibacter. The strain grew at 28-37 °C (optimum, 37 °C), at pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-0.5 % (w/v, optimum, 0.5 %) NaCl. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids and MK-7 as the predominant menaquinone. The polar lipid profile revealed that the presence of phosphatidylethanolamine, aminoglycophospholipid, two unidentified aminolipids and two unidentified lipids. The DNA G+C content of the strain was 49.1 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain TX0661T represents a novel species in the genus Flavisolibacter, for which the name Flavisolibactermetallilatus sp. nov. (=KACC 19145T=KCTC 52779T=NBRC 111784T) is proposed.

Research Article Hierarchical outcrossing among and within fruits in Bertholletia excelsa Bonpl. (Lecythidaceae) open-pollinated seeds

Knowing the mating patterns is important to determine the number of trees necessary for seed collection for conservation ex situ, tree breeding and environmental reforestation purposes. We investigated B. excelsa individuals and fruits, to check mating system index variations in a population by using open-pollinated seeds which were hierarchically sampled within and among fruits from nine trees genotyped for ten microsatellite loci. Outcrossing rate ( )changed between trees (0.49–1.0) and fruits (0.53–1.0), but seeds were predominantly produced by outcrossing (0.92) at mean population level. Mating between related trees ( ) was detected in six trees (0.04–0.08) and in 32 fruits in trees (0.03–0.22), thus it suggests that the population presented some related trees in our intra-population spatial genetic structure. Individual fixation index values of seed trees ( ) were lower than the seedling fixation index values ( ), fact that suggests the selection against inbred individuals between the seed and adult stages. The correlated mating showed that seeds sampled at population level were predominantly composed of half-sibs (66%) and full-sibs (20%). Paternity correlation was significantly higher within ( ) than among ( ) fruits at population level, mostly in individual trees. Results evidenced that mating was not random due to self-fertilization, to mating between related trees and correlated mating, and families comprised different relatedness levels such as half-sibs, full-sibs, self-sibs and self-half-sibs; some cases, mating presented inbreeding. These results were addressed to discuss strategies for seed collection applied to conservation ex situ, tree breeding and environmental reforestation.

A tutorial of diverse genome analysis tools found in the CoGe web-platform usingPlasmodiumspp. as a model

Integrated platforms for storage, management, analysis and sharing of large quantities of omics data have become fundamental to comparative genomics. CoGe (https://genomevolution.org/coge/) is an online platform designed to manage and study genomic data, enabling both data- and hypothesis-driven comparative genomics. CoGe’s tools and resources can be used to organize and analyse both publicly available and private genomic data from any species. Here, we demonstrate the capabilities of CoGe through three example workflows using 17 Plasmodium genomes as a model. Plasmodium genomes present unique challenges for comparative genomics due to their rapidly evolving and highly variable genomic AT/GC content. These example workflows are intended to serve as templates to help guide researchers who would like to use CoGe to examine diverse aspects of genome evolution. In the first workflow, trends in genome composition and amino acid usage are explored. In the second, changes in genome structure and the distribution of synonymous (Ks) and non-synonymous (Kn) substitution values are evaluated across species with different levels of evolutionary relatedness. In the third workflow, microsyntenic analyses of multigene families’ genomic organization are conducted using two Plasmodium-specific gene families—serine repeat antigen, and cytoadherence-linked asexual gene—as models. In general, these example workflows show how to achieve quick, reproducible and shareable results using the CoGe platform. We were able to replicate previously published results, as well as leverage CoGe’s tools and resources to gain additional insight into various aspects of Plasmodium genome evolution. Our results highlight the usefulness of the CoGe platform, particularly in understanding complex features of genome evolution. Database URL: https://genomevolution.org/coge/

Uloga industrijskih faktora u optimalnoj strukturi kapitala - empirijska studija o proizvodnim preduzećima iz Indonezije

The objective of this study is to improve the model of optimal capital structure. This research aims to investigate the role of the industrial factors on the optimal capital structure proxy by including industry factors in the existing model and using the company characteristic variables as control variables. This research applies seven industrial variables: Number of Firms in Industry (NFI), Industry Competitive Dynamic (ICD), Firm Response to Industry Competitive (FRI), Numbers of Employees in an Industry (NEI), Employees' Share of Firm Quasi Rents (ESQ), Category of Product Diversification (CPD), and Diversification level of Relatedness (DRD). This research determines whether the proposed proxy in this research is better than the two other proxies. The testing procedure is designed to replicate the procedure of Farhat (2003). The data used in the study consist of 83 companies from 13 industries listed on IDX for the period of 2001-2014. The results showed that the industry variables can improve the existing optimal capital structure proxies. This finding contributes to the industry in that it can improve the dynamic trade-off model of capital structure.

Commentary: Family Member Well-Being in the Kinship Enterprise: A Self-Determination Perspective

Nordstrom and Jennings (2017) provide an in-depth view of the Hutterite Brethren community to theorize family business practices and their association with familial well-being. Drawing from self-determination theory, we extend their model to provide additional theoretical development regarding the role of task and enterprise practices in satisfying basic needs (autonomy, competence, and relatedness), promoting motivation, and fostering family member well-being. Although the Hutterite community’s practices likely facilitate high levels of competence and relatedness, there is potential for autonomy need deficits. As such, we address areas for future research regarding need fulfillment and well-being in family businesses.

Marine Macrophyte Detritus and Degradation: the Role of Intraspecific Genetic Variation

Intraspecific genetic diversity influences the primary production and biomass of coastal marine foundation plants. The majority of their primary production ends up as detritus, yet the relationship between their intraspecific genetic diversity and detritus-based functions has rarely been considered. We addressed the relationship between these functions (detritus standing stock, degradation, sediment ammonium production) and genotypic diversity (richness, evenness, relatedness) in eelgrass (Zostera marina L.), a widely distributed coastal foundation plant, grown in the field at different levels of genotypic richness and relatedness. The functions were largely insensitive to the genotypic diversity, density, and biomass of the living plants in a plot, which suggests that changes in eelgrass genotypic diversity have minimal effects on these important functions and their consequences ranging from trophic support to carbon sequestration. Instead, detritus-based functions are perhaps more related to the sediment environment, the genotypic composition of the detritus itself, and macro- and microscopic detritus consumers.

Kin competition accelerates experimental range expansion in an arthropod herbivore.

With ongoing global change, life is continuously forced to move to novel areas, which leads to dynamically changing species ranges. As dispersal is central to range dynamics, factors promoting fast and distant dispersal are key to understanding and predicting species ranges. During range expansions, genetic variation is depleted at the expanding front. Such conditions should reduce evolutionary potential, while increasing kin competition. Organisms able to recognise relatives may be able to assess increased levels of relatedness at expanding range margins and to increase their dispersal in a plastic manner. Using individual-based simulations and experimental range expansions of a spider mite, we demonstrate that plastic responses to kin structure can be at least as important as evolution in driving range expansion speed. Because recognition of kin or kind is increasingly documented across the tree of life, we anticipate it to be a highly important but neglected driver of range expansions.

How Social Structure Drives the Population Dynamics of the Common Vampire Bat (Desmodus rotundus, Phyllostomidae).

Social systems are major drivers of population structure and gene flow, with important effects on dynamics and dispersal of associated populations of parasites. Among bats, the common vampire bat (Desmodus rotundus) has likely one of the most complex social structures. Using autosomal and mitochondrial markers on vampires from Mexico, French Guiana, and North Brazil, from both roosting and foraging areas, we observed an isolation by distance at the wider scale and lower but significant differentiation between closer populations (<50 km). All populations had a low level of relatedness and showed deviations from Hardy-Weinberg equilibrium and a low but significant inbreeding coefficient. The associated heterozygote deficiency was likely related to a Wahlund effect and to cryptic structures, reflecting social groups living in syntopy, both in roosting and foraging areas, with only limited admixture. Discrepancy between mitochondrial and nuclear markers suggests female philopatry and higher dispersal rates in males, associated with peripheral positions in the groups. Vampires are also the main neotropical reservoir for rabies virus, one of the main lethal pathogens for humans. Female social behaviors and trophallaxis may favor a rapid spread of virus to related and unrelated offspring and females. The high dispersal capacity of males may explain the wider circulation of viruses and the inefficacy of bat population controls. In such opportunistic species, gene connectivity should be considered for management decision making. Strategies such as culling could induce immigration of bats from neighboring colonies to fill vacant roosts and feeding areas, associated with the dispersal of viral strains.

Genetic Diversity in Drumstick of Andaman Islands and Their Relatedness with Probable Introduction Sites from Mainland India

The study investigated genetic diversity in Moringa oleifera Lam. samples (63) from nine islands in Andaman and Nicobar Islands (India) and their relatedness with samples (5) from their probable source regions in mainland India. The polymerase chain reaction analysis with polymorphic random fragment polymorphic DNA (RAPD) (5) and inter simple sequence repeat (ISSR) (20) markers generated 987 and 4190 amplicons, respectively. The RAPD analysis resulted into two main and eight sub-clusters and ISSR markers generated two main and five sub-clusters. Extent of similarity in 68 samples was revealed to be 49% by RAPDs to 53% by ISSR markers. Average polymorphism information content (PIC) value ranged from 0.47 to 0.50 for the studied markers. Maximum collections from the islands were grouped along with samples from Tamil Nadu, Andhra Pradesh and Kerala which suggest high level of genetic relatedness. The information on influence of ‘isle factor’ in genetic divergence of introduced drumsticks is useful for continuance of studies on genetic changes for adaptation.

Inbreeding, but not seed availability, affects dispersal and reproductive success in a seed-inhabiting social beetle

Societies based on family groups have flexible social structures, where genetic relatedness and ecological or demographic factors exert pronounced influence on the social organization. Individual decisions that play an important role in determining the degree of cooperation and resulting social structure include whether to disperse from the natal patch, to breed within the group, or to help rear the young. We investigated individual decisions regarding dispersal and possible cooperation in offspring rearing using the date stone beetle, Coccotrypes dactyliperda (Scolytidae). In this species, cooperative breeding is suggested by the observation that genetically similar beetles share galleries in a single seed (stone) over several generations. We used beetles from two populations to create offspring of higher and lower relatedness, and provided them with high and low availability of date seeds as food and alternative breeding sites for dispersing individuals. We found that care of the eggs by adult females is obligate for offspring development. Seed availability did not affect individual behaviors, but dispersal of inbred beetles was lower compared to outbred individuals. Although the number of eggs did not differ between breeding treatments, more offspring were found in colonies of inbred females, indicating either a greater level of cooperation or reduced conflict in the inbred beetles. Taken together, these results emphasize the importance of relatedness among individuals in determining the social strategy and the potential reproductive output of a colony. The evolution of cooperative group living is often ascribed to two main factors: high relatedness, promoting indirect fitness benefits, and environmental constraints on dispersal. We investigated the influence of relatedness between individuals and food and breeding site availability in the habitat on individual decisions relating to dispersal and reproductive success in the date stone beetle, Coccotrypes dactyliperda. The beetles share galleries in the seed (stone), and several generations may occupy a single seed. We found more independent young and fewer dispersers in inbred colonies than in outbred colonies, but expected food availability (i.e., additional dates in the surroundings) had no influence on dispersal or reproductive success. We suggest that colony social organization in this species is strongly influenced by the level of relatedness among colony members.

Albirhodobacter confluentis sp. nov., isolated from an estuary.

A Gram-stain-negative and strictly aerobic, moderately halophilic bacterium, designated strain S1-47T, was isolated from estuary sediment in South Korea. Cells were non-motile rods showing oxidase- and catalase-positive activities. Growth was observed at 10-30 °C (optimum, 25 °C), at pH 5.0-8.0 (optimum, pH 6.0-7.0) and in the presence of 0-6.0 % (w/v) NaCl (optimum, 2.0 %). Strain S1-47T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as major cellular fatty acids and ubiquinone-10 as the sole isoprenoid quinone. Phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and three unidentified lipids were detected as polar lipids. The G+C content of the genomic DNA was 69.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-47T formed a tight phylogenetic lineage with Albirhodobacter marinus N9T. Strain S1-47T was most closely related to Albirhodobactermarinus N9T with a 99.4 % 16S rRNA gene sequence similarity. DNA-DNA relatedness levels between strain S1-47T and the type strain of Albirhodobactermarinus were 49.8-52.2 %. Based on the phenotypic, chemotaxonomic and molecular features, strain S1-47T clearly represents a novel species of the genus Albirhodobacter, for which the name Albirhodobacter confluentis sp. nov. is proposed. The type strain is S1-47T (=KACC 18804T=JCM 31536T).

Mucilaginibacter panaciglaebae sp. nov., isolated from soil of a ginseng field.

A Gram-reaction-negative, strictly aerobic, non-motile and rod-shaped bacterium, designated strain BXN5-31T, was isolated from soil of a ginseng field, and its taxonomic position was investigated using a polyphasic approach. Strain BXN5-31T grew at 18-37 °C and at pH 6.0-8.0 on R2A medium. Based on 16S rRNA gene sequence similarity, strain BXN5-31T was shown to belong to the genus Mucilaginibacter and was closely related to Mucilaginibactersoyangensis HME6664T, Mucilaginibacterximonensis XM-003T and Mucilaginibacterpuniceus WS71T. The DNA G+C content was 43.6 %. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The DNA-DNA hybridization values between strain BXN5-31T and three reference strains (M. soyangensis HME6664T, M. ximonensis XM-003T and M. puniceus WS71T) were 9.4±1.9, 8.2±1.3 and 5.7±0.7 %, respectively. The DNA G+C content and chemotaxonomic data supported the affiliation of strain BXN5-31T to the genus Mucilaginibacter. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness allowed the phenotypic and genotypic differentiation of strain BXN5-31T from recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter panaciglaebae sp. nov. is proposed. The type strain is BXN5-31T (=KACC 14957T=JCM 17085T).

The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan

From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to ∼300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P.vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.

Genetic Mark–Recapture Improves Estimates of Maternity Colony Size for Indiana Bats

Abstract Genetic mark–recapture methods are increasingly being used to estimate demographic parameters in species where traditional techniques are problematic or imprecise. The federally endangered Indiana bat Myotis sodalis has declined dramatically and threats such as white-nose syndrome continue to afflict this species. To date, important demographic information for Indiana bats has been difficult to estimate precisely using traditional techniques such as emergence counts. Successful management and protection of Indiana bats requires better methods to estimate population sizes and survival rates throughout the year, particularly during summer when these bats reproduce and are widely dispersed away from their winter hibernacula. In addition, the familial makeup of maternity colonies is unknown, yet important for understanding local and regional population dynamics. We had four objectives in this study. For the first two objectives we investigated the potential use of DNA from fecal samples (fecal DNA) collected at roosts to obtain genetically based mark–recapture estimates of 1) colony size and 2) survival rates, for an Indiana bat maternity colony in Indianapolis, Indiana. The third objective was to compare our genetically based colony-size estimates with emergence counts conducted at the same roost tree to evaluate the genetic mark–recapture method. Our fourth objective was to use fecal DNA to estimate levels of relatedness among individuals sampled at the roost. In the summer of 2008, we collected fecal pellets and conducted emergence counts at a prominent roost tree during three time periods each lasting 7 or 8 d. We genotyped fecal DNA using five highly polymorphic microsatellite loci to identify individuals and used a robust-design mark–recapture approach to estimate survival rates as well as colony size at the roost tree. Emergence count estimates at the roost tree ranged from 100 to 215, whereas genetic mark–recapture estimates were higher, ranging from 122 to 266 and more precise. Apparent survival was 0.994 (SE = 0.04) between sampling periods suggesting that few bats died or permanently emigrated during the course of the study. Relatedness estimates, r, between all pairs of individuals averaged 0.055 ranging from 0 to 0.779, indicating that most individuals were not closely related. We demonstrate here the promise of using fecal DNA to estimate demographic information for Indiana bats and potentially other bat species.

Gordonia phthalatica sp. nov., a di-n-butyl phthalate-degrading bacterium isolated from activated sludge.

A phthalate esters-degrading bacterial strain, designated QH-11T, was isolated from an activated sludge wastewater treatment plant in Beijing, PR China. The cells were aerobic, Gram-stain-positive, non-motile, catalase-positive, oxidase-negative, short rods and formed white colonies on trypticase soy agar. This isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained arabinose and ribose. Diphosphatidylglycerol and phosphatidylethanolamine were the predominant polar lipids. According to the results of full-length of 16S rRNA gene sequence analysis, QH-11T represented a member of the genus Gordonia and showed the highest sequence similarity to Gordonia hydrophobica DSM 44015T (99.2 %), but was distinguishable by a low level of DNA-DNA relatedness (37.8 %). Genome-based comparisons indicated a clear distinction from the top ten most similar type strains (16S rRNA gene sequence) with pairwise average nucleotide identities (ANI) between 74.6 and 83.4 %. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had 56 to 62 carbon atoms, and the major fatty acids were C16 : 0 (33.3 %), C17 : 1ω8c (23.4 %) and C18 : 1ω9c (17.9 %). The DNA G+C content was 68.0 mol%. On the basis of the results of DNA-DNA hybridization, ANI and physiological and biochemical tests, it is proposed that QH-11T represents a novel species of the genus Gordonia, for which the name Gordonia phthalatica sp. nov. is proposed. The type strain is QH-11T (CICC 24107T =KCTC 39933T).

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

Performance and business relatedness as drivers of exit decision: A study of MNCs from an emerging country

Research SummaryThis study examines the exit behavior of emerging market MNCs in the context of the parent company (PC)‐foreign affiliate (FA) relationship. Specifically, we consider business relatedness as a moderating variable and examine its impact on the relationship between an FA’s international performance and its exit decision from a foreign market. Our results, based on data collected from multiple informants in 180 Chinese firms, indicate that product relatedness and intangible resource relatedness have different moderating impacts on the FA performance‐FA exit decision relationship. Implications of these findings, along with the limitations of the study, are discussed.Managerial SummaryAlthough the research on international entry and expansion is particularly important, an aspect that has been largely ignored in the literature is the exit behavior of firms. This study examines whether the extent to which a foreign subsidiary is similar to its parent's core business may influence the firm's exit decision. The findings indicate that managers are more likely to exit a poorly performing FA if there is a high (vs. low) level of product relatedness between the FA and its PC's core business. The results also suggest that intangible resource relatedness exerts a different contingent effect on the FA performance‐FA exit relationship than does product relatedness.

Sphingomonas agri sp. nov., a bacterium isolated from soil.

A Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06T) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06T was observed to grow optimally at 30 °C and at pH 6.5-7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06T belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5T (97.4 % similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C18 : 1ω6c, C18 : 0 3-OH and C16 : 0)] supported the affiliation of strain HKS-06T to the genus Sphingomonas. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness [between strain HKS06T and S. lutea JS5T (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06T from recognized species of the genus Sphingomonas. The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06T (=KACC 18880T=LMG 29563T).

Sphingobacterium humi sp. nov., isolated from soil.

A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).