C H A P T E R

1
Arthrobacter
Pratiti Roy, Ashok Kumar
Department of Genetics and Plant Breeding (Plant Biotechnology), Rajiv Gandhi South
Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India

1. Introduction

Arthrobacter is a group of pleomorphic bacteria, ubiquitous in origin with effective roles in

agriculture. This group of bacteria is difficult for stringent classification as the members
provide dynamism in shape due to nutrient availability and resources that they utilize for
growth. A general classification can be made based on the 16S rRNA sequence phylogeny
data by which Arthrobacter genus has been subdivided into 11 major groups as Arthrobacter
aurescens, Arthrobacter globiformis, Arthrobacter pascens, Arthrobacter oryzae, Arthrobacter humicola,
Arthrobacter oxydans, Arthrobacter protophormiae, Arthrobacter sulfureus, Arthrobacter citreus,
Arthrobacter agilis, Arthrobacter psychrolactophilus, Arthrobacter pigmenti, Arthrobacter albus/cum-
minsii, and Sinomonas soli (Busse et al., 2012). A chemotaxonomic classification has been done
based on the A3a or A4a peptidoglycan types, the former showing a quinone system and with
MK9-2(H), whereas the latter bears unsaturated menaquinones (MK-8, MK-9, and MK-10)
mostly in the cell walls (Busse et al., 2012; Schleifer and Kandler, 1972). The maximum species
of this genus harbors the cellular fatty acids (Schleifer and Kandler, 1972). The bacteria may be
rods changing to coccoid in the stationary phase from the growth (log) phase and coryneform
(comma shaped) due to many reasons. These bacteria can effectively utilize organic and
inorganic compounds as a substrate of metabolism, thus acting as a tool for bioremediation
in agriculture. Arthrobacter has been also reported with plant growth-promoting activity,
mainly the soil dwellers that form a greater group of rhizobacteria. Although, some groups
of Arthrobacter have been isolated from the phyllosphere, as scientists predict them to be
transported by rain splashes from soil or through any other means of contact to the phyllo-
sphere (Scheublin and Leveau, 2013). Actinobacteria, members of the genus Arthrobacter, are
of massive significance as they are among the most frequently isolated bacteria and are
commonly isolated from soils and water contaminated with industrial chemicals and radioac-
tive materials (Dsouza et al., 2015). It has also been reported that up till 2015, there have been
complete and published genomes for just six species, namely A. aurescens TC1, Arthrobacter
sp. FB24, Arthrobacter chlorophenolicus A6, A. phenanthrenivorans Sphe3, A. arilaitensis re117,

Beneficial Microbes in Agro-Ecology

https://doi.org/10.1016/B978-0-12-823414-3.00001-0 3 © 2020 Elsevier Inc. All rights reserved.
4 1. Arthrobacter

and A. nitroguajacolicus Rue61a. The genome sequences of seven Antarctic Arthrobacter isolates
have been compared with the available seven temperate isolates (Pagani et al., 2012). Fewer
genes could be identified from the polar ones but the “final pan-genome” of Arthrobacter
was found to comprise 14,902 sequences, indicating an array of accessory genes with great di-
versity. Several strategies for adapting in the colder climes was found in these species, reported
by the presence of rpoE, fliA, rpoD, sodA, sodC, katE, katG, bcp, osmC, ohr, trx, trxB, trxA, soxR,
glgA, glgB, glgC, rtB, crtI, crtEB, idi, crtE, glgP, glgX, otsA, otsB, treS, treY, treZ, proV, proW,
proX, csd, capA, nusA, pnp, rbfA, infA, infB, crtYe, crtYf, and desA genes.

2. Taxonomy

Conn and Dimmick (1947) had proposed the genus Arthrobacter that included Arthrobacter
globiforme, also known as A. globiformis, A. tumescens, and Arthrobacter helvolum on the basis
of morphology, cultural characteristics, and physiology of the bacteria. As per the description
cited by Conn and Dimmick (1947) or Keddie (1974), 16 more species were reported by 1995:
A. aurescens, Arthrobacter crystallopoietes Arthrobacter nicotianae, A. citreus, Arthrobacter histidino-
lovorans, Arthrobacter mysorens, Arthrobacter nicotinivorans, Arthrobacter polychromogenes, Arthro-
bacter ramosus, A. protophormiae, Arthrobacter uratoxydans, A. sulfureus, Arthrobacter ureafaciens,
A. pascens, Arthrobacter oxydans, and Arthrobacter ilicis (Busse, 2016). A. agilis was included in
Arthrobacter genus (Koch et al., 1995). Later, 51 more species were described, as of 2012, and
novel species like Arthrobacter cryoconiti (Margesin et al., 2012), Arthrobacter siccitolerans
(SantaCruz-Calvo et al., 2013), Arthrobacter gyeryongensis (Hoang et al., 2014), and Arthrobacter
cupressi (Zhang et al., 2012) were added.

3. Isolation and identification of Arthrobacter genus

Arthrobacter species are isolated from soil and water, from a range of varying climates in
the tropics and temperate zones to even harsher places of Antarctica and metal-
accumulated, polluted lands. Arthrobacter species has been isolated from the phyllosphere
also, and their epiphytotic fitness has been demonstrated in comparison to bacterial epiphyte
Pantoea agglomerans (Scheublin and Leveau, 2013). Phyllosphere bacterial isolation is done by
collection of leaves from infected plants washed in phosphate-buffered saline and incubated
in Brunner mineral media at 25
C with shaking conditions. After 2 weeks of enrichment,
serial dilutions are performed, followed by plating in tryptone soya agar and resteaking twice
for ensuring a pure culture. 16S rRNA gene amplification is done using suitable primers, and
the new sequence is compared to the available Arthrobacter sequences from suitable data-
bases. Unique sequences obtained are submitted as new reports, and older ones are conferred
for further analysis.
Isolation from soil is elaborate and needs solubilizing soil in sterile saline solution and
performing serial dilutions to obtain colonies in liquid or solid media (R2A Agar and several
other media are used). Again, 16S rRNA sequencing is done to confirm the bacterial strain,
and further phylogenetic analysis is carried out to reveal the relationship among various
bacterial species and strains. Basic tests are generally performed like cell morphology test,
Gram Test, Catalase Test, Oxidase Test, sodium chloride (NaCl) tolerance, and pH tolerance

I. Bacteria
 5. Siderophore production and metal solubilization by Arthrobacter 5
tests, and various biochemical tests like hydrolysis of casein, Voges-Proskauer, Indole
production test, hydrolysis of gelatine, starch, aesculin, DNA, cellulose, Tween 80, Tween
20, and urea tests, along with incubation in different types of media like MacConkey agar,
tryptone soy agar, Luria Bertani agar, marine agar, yeast mold agar, and nutrient agar
(Park et al., 2014). Any novel species reported is analyzed thoroughly before submission of
data, and the DNA GþC content of the new strain is determined (Mesbah et al., 1989).
Reversed phase HPLC analysis is done to analyze the nucleosides following DNA hydrolysis,
and DNA-DNA relatedness is confirmed by hybridization experiments (Ezaki et al., 1989).
Cell wall analysis, fatty acid profile, amino acid and peptide analysis, isoprenoid quinine
analysis, and several other enzyme activity tests are noted (Park et al., 2014). Thus, to
conclude, any bacterial isolate, whether from rhizospheric soil or the phyllosphere, is
thoroughly evaluated before its role is judged in agricultural spheres.

4. Arthrobacter as a plant growth-promoting rhizobacteria

The association of diverse strains of Arthrobacter with different plants reveal the beneficial
implications of the latter in plant growth and yield. In plants that are grown in saline,
polluted, drought prone, and low-nutritive agricultural soils, Arthrobacter species has played
eminent roles in protecting plants from abiotic stresses and has also helped in improving
plant health and yield, thus proving itself as a notable member of the rhizosphere microflora
(Krishnan et al., 2016). The following Arthrobacter species were able to produce auxin:
A. globiformis, A. pascens, A. aurescens, A. tumescens, A. citreus, and A. atrocyaneous. It was
experimentally proven by conversion of tryptophan to indole 3-acetic acid. IAA, as we
know, is responsible for the growth and development of higher plants, so Arthrobacter may
act as a promising Plant Growth Promoting Rhizobacteria (PGPR) in agricultural land (Katz-
nelson and Sirois, 1961).
However, A. cupressi, A. bambusae, A. humicola, A. oryza, A. siccitolerans, and
A. gyeryongensis, having been isolated from rhizospheric soil, did not show any plant
growth-promoting properties, and it also was reported that the conglomeration of Arthro-
bacter species with various crops growing under stressful conditions and its significance
are yet to be delved into in detail in spite of their immense roles toward maintenance of plant
health (Krishnan et al., 2016). Scientists have recently discovered Arthrobacter pokkalii sp. nov
from pokkali rice (a highly saline-tolerant rice variety) that was able to synthesize IAA (indole
3-acetic acid) by utilizing L-tryptophan and could grow on ACC (1-aminocyclopropane-1-
carboxylic acid), which proved the ability of the bacteria to utilize ACC under abiotic stresses
to save the plant from the adverse effects of ethylene. This strain is also able to synthesize
siderophores, form biofilm on the walls of the glass tube, effectively growing in an acid saline
environment of pH 5.5 and 8% NaCl and also shows growth in polyethylene glycol (PEG)
media, thereby proving its ability to sustain drought conditions. This strain, however, did
not show any evidence of nitrogen utilization or for nif H gene amplification.

5. Siderophore production and metal solubilization by Arthrobacter

Rare earth elements consist of the 14 lanthanides, including yttrium (Y) besides cerium,
gadolinium, neodymium, samarium, ytterbium, holmium, lanthanum, and so on.

I. Bacteria
6 1. Arthrobacter

Microorganisms have the ability to biosorp these metals and sequester them, in many cases,
in their cell walls via novel pathways with the aid of their genes (Emmanuel et al., 2010; And-
ras et al., 2000). The microorganisms can chelate the various divalent and trivalent cations as
the polycarboxylic acids and aminocarboxylic acids can form stable complexes. Metal sidero-
phores are very specific in action. Specific membrane proteins actively transport the com-
plexes, and Fe release occurs either at the membrane or within the cytoplasm (Urrutia
et al., 1992).

6. Role of Arthrobacter in bioremediation

The word bioremediation refers to the breaking down of environmental pollutants by a
group of microbial consortiums, plants, or a combination of both (Bjerketorp et al., 2018).
This chapter evokes the idea of bacterial degradation of toxic compounds from soil and
conversion to lesser toxic intermediates to be used up by plants or other microbiota. Instances
of bioremediation by the various species and strains of Arthrobacter have been tabulated in
Table 1.1. The importance of each bacterial strain or species in an agri-ecosystem has been
elucidated by mentioning its major degrading role. This has paved its path for sustainable
agriculture and development in a global context.
The latest researches have focused on the biodegrading ability of Arthrobacter strains
owing to the need of less expensive and technically less challenging means of remediation
(Table 1.2). Thus, studies have been conducted with the 4-chlorophenol degrading Arthro-
bacter cholophenolicus A6 in soil microcosms to check the degrading ability and its effective-
ness in the environment (Bjerketorp et al., 2018). The A6 strain is also able to degrade a
large proportion of 4-chlorophenol in soil at colder climates, as demonstrated (Bjerketorp
et al., 2004). 4-Chlorophenol degradation via hydroxyquinol pathway is a novel path for
aerobic degradation by Arthrobacter chlorophenolicus A6 and the group of cph gene cluster
was identified showing cphA-I and cphA-II encoding functional hydroxyquinol 1, 2-

TABLE 1.1 Taxonomic hierarchy of Arthrobacter.

Rank Name Reference

Kingdom Bacteria Cavalier-Smith (2002)

Subkingdom Posibacteria Cavalier-Smith (2002)

Phylum Actinobacteria Cavalier-Smith (2002)

Class Arthrobacteria Cavalier-Smith (2002)
Subclass Actinobacteridae Stackebrandt et al. (1997)
Order Actinomycetales Oren (2017)
Suborder Micrococcineae Stackebrandt et al. (1997)
Family Micrococcaceae Pribram (1929)

Genus Arthrobacter Conn and Dimmick (1947), Koch et al. (1995)

I. Bacteria
 6. Role of Arthrobacter in bioremediation 7
TABLE 1.2 Role of Arthrobacter strains on bioremediation.
Arthrobacter species Role References

Arthrobacter Can remove high levels of toxic pollutant 4-chlorophenol from Bjerketorp et al.
chlorophenolicus A6 contaminated soil (2018)
Arthrobacter sp. Grow in presence of toxic hexavalent chromium and bioremediation Megharaj et al.
(2003)
Arthrobacter aurescens Atrazine utilization from industrial wastewater Li et al. (2008)
TC1
Arthrobacter icotianae Can degrade pentachloronitrobenzene (PCNB), dichlorodiphenyl Wang et al.
trichloroethane, hexachlorocyclohexane, cypermethrin, and cyhalothrin (2015)
Arthrobacter Complex hydrocarbon, herbicide, and pesticide degrading ability; iron Joshi et al.
crystallopoietes strain uptake and phenyl acetic acid degradation ability as revealed by its (2013)
BAB-32 whole genome sequencing

Arthrobacter Biodegradation of p-nitrophenol Labana et al.

protophormiae RKJ100 (2005)

Arthrobacter luteolus Accumulation of rare earth elements by production of siderophore Emmanuel et al.
(2012)
Arthrobacter nicotianae Accumulation of higher amounts of Sm than other REEs from a Tsuruta (2006)
solution containing 6 LREEs
Arthrobacter sp. Atrazine-degradation Wang and Xie
(2012)
Arthrobacter sp. strain Polychlorinated biphenyl degradation by carvone and salicylic acid Singer et al.
B1B (2000)
Arthrobacter strain DAT1 Atrazine biodegradation Xie et al. (2013)
Arthrobacter sp. strain Atrazine degradation Parag et al.
MCM B-436 (2007)
Arthrobacter strain SD3- Simazine biodegradation Guo et al. (2014)
25
Arthrobacter sp. strain Polychlorinated biphenyl biodegradation Gilbert and
B1B Crowley (1997)
Arthrobacter sp. WZ2 Chromium (VI) reduction Xiao et al. (2017)
Arthrobacter sp. W1 Degradation of coking wastewater containing carbazole, dibenzofuran, Shi et al. (2014)
dibenzothiophene, and naphthalene

dioxygenases, which are critical in 4-chlorophenol degradation (Nordin et al., 2005). Arthro-
bacter HB5, a notable atrazine degrading strain of Arthrobacter, isolated from industrial waste-
water aids in the conversion of atrazine to hydroxyatrazine and the latter to cyanuric acid
(Wang et al., 2015). This is how the atrazine-polluted soil may be cleared from its harmful
effects, thus paving the way for the maintenance of soil sustainability. Arthrobacter AD26 is

I. Bacteria
8 1. Arthrobacter

also a potent atrazine degrader and helps in bioremediation of contaminated soils by 98%
with the help of its trzN and atzBC genes, operative at a soil with 300 mg/kg levels of atrazine
contamination at 26
C for 20 days, thus being a good candidate for bioremediation programs
(Li et al., 2008). Among other atrazine degrading strains, Arthrobacter nicotinovorans HIM is
able to degrade simazine, terbuthylazine, propazine, cyanazine, and prometryn besides atra-
zine to cyanuric acid. The atzABC genes have been elucidated in this strain to find out the
underlying mechanisms of atrazine degradation by the bacterial isolate.
PNP (p-nitrophenol), entailed as a hazardous substance, is utilized by Arthrobacter species
strain JS443 (Perry and Zylstra, 2007) and is degraded to 4-nitrocatechol by uninduced cells
and to nitrohydroquinone from m-nitrophenol by induced cells (Jain et al., 1994). The Npd
family of genes were expressed in E. coli cells to identify the related gene products. NpdA2
was found to be p-nitrophenol monooxygenase and NpdA1 was a reductase,NpdB a hydrox-
yquinol 1, 2-dioxygenase, and npdC a putative maleylacetate reductase gene (Perry and Zyl-
stra, 2007). Naphthalene, a carcinogenic benzenoid polycyclic aromatic compound, is a
priority pollutant that needs to be kept in check in nature. 1- and 2-methylnapthalene degra-
dation by Arthrobacter alpinus R3.8 genes for salicylate-1-monoxygenase, imidazole glycerol
phosphate synthase cyclase has been elucidated. 1, 4-dichlorobenzene degradation is aided
by enoyl-CA hydratase, aliphatic amidase amiE, nitrilotriacetate monooxygenase, and alka-
line phosphatise genes of the same Arthrobacter strain (Too et al., 2017).

7. Future prospects

Arthrobacter possesses a range of genes for heavy metal uptake and breaking down of
complex organic and inorganic compounds that may damage the environment. Several
such potential genes for different metal degradation may be integrated to form a transgene
and may be used under a suitable promoter and terminator to construct synthetic bacteria
with the potency to degrade different xenobiotics in different environments. Studies on
Arthrobacter simplex have demonstrated the biotransformation of steroid drug cortisone
acetate (CA) to prednisone acetate. Additional copies of ksdD gene, a gene for
3-ketosteroid-D1-dehydrogenase synthesis under the control of cat promoter, were trans-
ferred to the strain A. simplex 156, and a new recombinant strain M158 was formed that
showed higher CA biotransforming abilities (Zhang et al., 2013).

8. Conclusion

The ability of Arthrobacter to benefit plants under stressful conditions and various other
isolates to degrade complex compounds and sequester heavy metals is always a burgeoning
branch of research. Several pathways may be addressed to know the detailed mechanism of
how the stress-responsive genes perform within the organism and how that may be exploited
for human welfare. Agriculture is a sector of utmost importance and offers food security to all
the countries of the world; hence, microbiota related to plant growth and environmental

I. Bacteria
 References 9
management are indispensable for research. Arthrobacter sp. may be studied in depth for sus-
tainable agriculture for human welfare.

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 References 11
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I. Bacteria