Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

/pdf/analysis-of-1-000-type-strain-genomes-improves-taxonomic-345doatvi9.pdf

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes .

The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.

/pdf/genome-based-taxonomic-classification-of-bacteroidetes-5y671uumne.pdf

Genome-Based Taxonomic Classification of Bacteroidetes.

The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4170

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea.

Calcium precipitate induced aerobic granulation.

A Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated strain JJ013T, was isolated from an artificial lake in Jeollabuk-do, South Korea, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain JJ013T indicated that the isolate belonged to the family 
Flavobacteriaceae
and exhibited similarity levels of 96.6 % to the type strains of 
Flavobacterium cheonanense
and 
Flavobacterium koreense
and 96.5 % to the type strain of 
Flavobacterium chungnamense
. Growth was observed at 20–30 °C and pH 5.0–7.0. The major cellular fatty acids of the novel strain were iso-C15 : 0 (27.5 %), iso-C15 : 1 G (17.8 %), iso-C17 : 0 3-OH (9.4 %) and iso-C15 : 0 3-OH (9.2 %). Flexirubin-type pigments were present. The DNA G+C content of strain JJ013T was 33.9 mol%, the major respiratory quinone was menaquinone-6 (MK-6) and the major polyamine was sym-homospermidine. The polar lipid profile of the strain JJ013T consisted of a phosphatidylethanolamine (PE), two unknown aminolipids (AL1–2), three unidentified lipid (L1–3) and an unknown glycolipid (GL). On the basis of the morphological and physiological properties and biochemical evidence presented, it is concluded that strain JJ013T represents a novel species of the genus 
Flavobacterium
, for which the name Flavobacterium aciduliphilum sp. nov. is proposed; the type strain is JJ013T ( = KACC 16594T = JCM 18211T). Since C15 : 0, which is known as a predominant fatty acid of the genus 
Flavobacterium
was not detected in the novel strain and other reference strains, we propose an emended description of the genus 
Flavobacterium
.

Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium

A Gram-negative, strictly aerobic, yellow-pigmented rod, designated DK69T, was isolated from soil collected from the waste liquid treatment facility of Bafeng Pharmaceutical Company in the city of Enshi, Hubei Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain DK69T in the genus 
Flavobacterium
of the family 
Flavobacteriaceae
. The highest 16S rRNA gene sequence similarities were found with 
Flavobacterium cauense
R2A-7T (96.9 %), 
Flavobacterium saliperosum
AS 1.3801T (96.3 %) and 
Flavobacterium suncheonense
GH29-5T (95.7 %). The major fatty acids (≥5 %) were iso-C15 : 0, iso-C17 : 1ω9c, C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 34.4 mol%. Strain DK69T represents a novel species of the genus 
Flavobacterium
, for which the name Flavobacterium enshiense sp. nov. is proposed. The type strain is DK69T ( = CCTCC AB 2011144T  = KCTC 23775T). Emended descriptions of the genus 
Flavobacterium
and 
Flavobacterium cauense
, 
Flavobacterium saliperosum
and 
Flavobacterium suncheonense
are also proposed.

Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense

A Gram-staining-negative, aerobic, rod-shaped bacterium (CF5-1T) was isolated from Hongshan Iron Mine, Daye City, Hubei province, China. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c alcohol and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major respiratory quinone was Q-8. The genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CF5-1T was most closely related to 
Arenimonas malthae
(95.3 % gene sequence similarity), 
Arenimonas oryziterrae
(94.7 %), 
Arenimonas donghaensis
(94.6 %) and 
Arenimonas composti
(94.5 %). A taxonomic study using a polyphasic approach showed that strain CF5-1T represents a novel species of the genus 
Arenimonas
, for which the name Arenimonas metalli sp. nov. is proposed. The type strain is CF5-1T ( = CGMCC 1.10787T = KCTC 23460T = CCTCC AB 2010449T).

Arenimonas metalli sp. nov., isolated from an iron mine.

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were 
Lysinibacillus massiliensis
CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), 
L. xylanilyticus
XDB9T (96.7 %), 
L. sinduriensis
JCM 15800T (96.2 %), 
L. odysseyi
NBRC 100172T (95.9 %) and 
L. boronitolerans
NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of 
L. massiliensis
and 
L. sinduriensis
were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus 
Lysinibacillus
, for which the name 
Lysinibacillus
manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).

http://www.ebmlab.org/upload/paper/ijs0504921.pdf

Lysinibacillus manganicus sp. nov., isolated from manganese mining soil.

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Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense

Arenimonas metalli sp. nov., isolated from an iron mine.

Lysinibacillus manganicus sp. nov., isolated from manganese mining soil.