Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region

PAN, HU; ZHOU, JIE; DAWA, ZHUOMA; DAI, YANNA; ZHANG, YIFAN; YANG, HUI; WANG, CHONG; LIU, HUHU; ZHOU, HUI; LU, XIANGYANG; TIAN, YUN

doi:10.33073/pjm-2021-008

Figures & Tables

The number and diversity of bacteria.A) The numbers of bacteria isolated from different media at 4° and 25°. B) Diversity of bacteria isolated from different culture media. C) Diversity of bacteria isolated from different temperature. D) The numbers of dominant species isolated from 4° and 25°.

Phylogenetic tree based on 16S rRNA gene sequences of soil isolates and related species.

Phylogenetic tree based on the16S rRNA gene sequences of new candidates and related species.

BLAST results based on 16S rRNA gene sequences of 77 bacterial species_

Strain number	Name of strain having the highest 16S rRNA gene similarity	The highest similarity (%)
T74^*	Actinoplanes digitatis IFO 12512	98.82
T203	Aeromicrobium ginsengisoli Gsoil 098	99.82
T96^*	Agromyces binzhouensis OAct353	98.62
T229^*	Agromyces humatus CD5	98.74
T805	Arthrobacter crystallopoietes DSM 20117	99.85
T763	Arthrobacter humicola KV-653	100
T65	Bacillus siamensis KCTC 13613	100
T94	Bacillus cereus ATCC 14579	100
T228^*	Bacillus drentensis LMG 21831	99.34
T59	Bacillus pumilus ATCC 7061	100
T115	Bacillus selenatarsenatis SF-1	99.6
T822	Dietzia kunjamensis subsp DSM 44907	99.86
T230	Exiguobacterium mexicanum 8NT	100
T183^*	Glycomyces algeriensis NRRL B-16327	98.9
T64	Gordonia otitidis NBRC 100426	100
T830^*	Hymenobacter humi DG31A	98.60
T769^*	Kaistia defluvii B6-12	99.72
T144	Kocuria sediminis FCS-11	99.43
T145	Kribbella albertanoniae BC640	100
T214^*	Kribbella catacumbae DSM 19601	99.6
T422	Kribbella karoonensis Q41	99.87
T823	Kytococcus schroeteri DSM 13884	99.73
T781	Leifsonia flava SYP-B2174	99.73
T146	Longispora urticae NEAU-PCY-3	99.88
T181^*	Luteimonas composti CC-YY255	98.9
T156	Macrococcus canis KM 45013	99.86
T489	Microbacterium maritypicum DSM 12512	99.55
T773	Microbacterium natoriense TNJL143-2	99.87
T804	Microbacterium phyllosphaerae DSM 13468	99.73
T133	Microbacterium thalassium IFO 16060	98.93
T226	Micrococcus luteus NCTC 2665	99.63
T47	Micromonospora cremea DSM 45599	99.87
T206	Micromonospora luteifusca GUI2	99.87
T197^*	Micromonospora palomenae NEAU-CX1	98.74
T92	Micromonospora saelicesensis Lupac 09	100
T786^*	Neorhizobium vignae CCBAU 05176	98.70
T62	Nocardia salmonicida subsp R89	99.47
T105^*	Nocardioides caeni MN8	98.01
T218	Paenibacillus odorifer DSM 15391	99.63
T608	Paenarthrobacter aurescens NBRC 12136	99.07
T236	Paenarthrobacter nitroguajacolicus G2-1	100
T808^*	Pararhizobium herbae CCBAU 83011	98.79
T209	Peribacillus simplex NBRC 15720	100
T811	Phyllobacterium ifriqiyense STM 370	100
T274^*	Phyllobacterium zundukense Tri-48	98.57
T63	Promicromonospora alba 1C-HV12	100
T193^*	Pseudarthrobacter siccitolerans 4J27	99.34
T755	Pseudomonas laurylsulfativorans AP3_22	99.73
T776	Pseudomonas lini CFBP 5737	100
T174^*	Pseudoxanthomonas sacheonensis BD-c54	99.34
T127^*	Rhodococcus jostii DSM 44719	99.32
T788	Rhodococcus qingshengii JCM 15477	100
T185^*	Skermanella aerolata 5416T-32	98.86
T93	Sphingopyxis fribergensis Kp5.2	99.87
T45	Staphylococcus caprae ATCC 35538	100
T61	Staphylococcus cohnii subsp ATCC 49330	100
T666	Streptomyces albogriseolus NRRL B-1305	100
T313	Streptomyces atroolivaceus NRRL ISP-5137	100
T234	Streptomyces bottropensis ATCC 25435	99.87
T130	Streptomyces caniferus NBRC 15389	99.87
T235	Streptomyces canus DSM 40017	99.73
T690	Streptomyces dioscori A217	99.47
T532	Streptomyces flavovirens NBRC 3716	99.85
T674^*	Streptomyces humidus NBRC 12877	98.8
T296	Streptomyces hydrogenans NBRC 13475	99.46
T219	Streptomyces hypolithicus HSM10	99.46
T426	Streptomyces kurssanovii NBRC 13192	99.6
T569	Streptomyces lunaelactis MM109	99.2
T348	Streptomyces niveus NRRL 2466	99.46
T84	Streptomyces phaeoluteigriseus DSM 41896	99.6
T581	Streptomyces turgidiscabies ATCC 700248	100
T110^*	Streptomyces xanthochromogenes NRRL B-5410	98.97
T100	Streptomyces xanthophaeus NRRL B-5414	99.71
T111^*	Terrabacter ginsengisoli Gsoil 653	99.19
T160	Umezawaea tangerina NRRL B-24463	99.18
T812	Variovorax boronicumulans BAM-48	99.47
T134^*	Yinghuangia seranimata YIM 45720	98.73

Isolation media_

Media	Composition
X1	peptone 2.0 g, yeast extract 0.5 g, FePO₄ · 4H₂O 0.1 g, MgSO₄ · 7H₂O 0.5 g, CaCO₃ 0.2 g, NaCl 0.5 g, agar 18.0 g, ddwater 1,000 ml, pH 7.0
R	peptone 10.0 g, yeast extract 5.0 g, maltose extract 5.0 g, casein amino acid 5.0 g, beef extract 2.0 g, glycerol 2.0 g, Tween-80 50.0 mg, MgSO₄ · 7H₂O 1.0 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.6
L1	NaCl 100.0 g, K₂HPO₄ 5.0 g, MgSO₄ · 7H₂O 7.5 g, hydrolyzed casein 1.0 g, yeast extract 5.0 g, Na₃C₆H₅O₇ · 2H₂O 3.0 g, FeSO₄ · 7H₂O 0.1 g, MnCl₂ · 4H₂O 0.1 g, ZnSO₄ · 7H₂O 0.1 g, agar 18.0 g, ddwater 1,000 ml, pH 7.0-8.0
ISP2	NaCl 100.0 g, dextrose 4.0 g, yeast extract 4.0 g, maltose extract 10.0 g, MgSO₄ · 7H₂O 0.5 g, CaCO₃ 2.0 g, FeSO₄ 10 mg, agar 18.0 g, ddwater 1,000 ml, pH 7.0-8.0
GW1	NaCl 100.0 g, casein 0.3 g, mannitol 1.0 g, NaHCO₃ 2.0 g, CaCO₃ 0.2 g, (NH₄)₂SO₄ 2.0 g, KNO₃ 2.0 g, K₂HPO₄1.0 g, MgSO₄ · 7H₂O 2.0 g, FeSO₄ 10.0 mg, Trace-salt 10.0 mg/l, Agar 18.0 g, ddwater 1,000 ml, pH natural
DSM372	NaCl 100.0 g, hydrolyzed casein 5.0 g, yeast extract 5.0 g, Na₃C₆H₅O₇ · 2H₂O 3.0 g, Na₂CO₃ · 10H₂O 8.0 g, NaC₅H₈NO₄ 1.0 g, KCl 2.0 g, MgSO₄ · 7H₂O 2.0 g, agar 18.0 g, ddwater 1,000 ml, pH natural
F1	glycerol 5.0 g, alanine 3.0 g, arginine 1.0 g, (NH₄)₂SO₄ 2.64 g, KH₂PO₄ 2.38 g, K₂HPO₄ 5.65 g, MgSO₄ · 7H₂O 1.0 g, CuSO₄ · 5H₂0 0.0064 g, FeSO₄ · 7H₂O 0.0011 g, MnCl₂ · 4H₂O 0.0079 g, ZnSO₄ · 7H₂O 0.0015 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
F2	MgSO₄ · 7H₂O 0.5 g, CaCO₃ 0.2 g, FeSO₄ 10.0 mg, NaCl 0.5 g, MnCl₂ · 4H₂O 1.4 g, Na₂MoO₄ · 2H₂O 0.39 g, Co(NO₃)₂ · 6H₂O 0.025 g, ZnSO₃ · 7H₂O 0.222 g, NaHCO₃ 2.0 g, NaH₂PO₄ · 2H₂O 0.05 g, agar 18.0 g, ddwater 1,000 ml, pH natural (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
M1	soluble starch 10.0 g, casein 0.3 g, KNO₃ 2.0 g, K₂HPO₄ 2.0 g, MgSO₄ · 7H₂O 0.05 g, FeSO₄ · 7H₂O 0.01 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
M5	yeast extract 4.0 g, soluble starch 15.0 g, K₂HPO₄ 1.0g, FeSO₄ · 7H₂O 0.01 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.6 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
M6	raffinose 10.0 g, L-histidine 1.0 g, MgSO₄ · 7H₂O 0.5 g, FeSO₄ · 7H₂O 0.01 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
M7	L-aspartic acid 0.1 g, peptone 2.0 g, sodium propionate 4.0 g, FeSO₄ · 7H₂O 0.01 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
M8	glycerine 6.0 ml, arginine 1.0 g, MgSO₄ · 7H₂O 0.5 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
HV	humic acid 1.0g, Na₂HPO₄ 0.5 g, KCl 1.7 g, MgSO₄ 0.5 g, FeSO₄ 0.01 g, CaCO₃ 0.02 g, agar 18.0 g, ddwater 1,000 ml, pH 7.2-7.4 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)
GS	soluble starch 20.0 g, NaCl 0.5 g, KNO₃ 1.0 g, K₂HPO₄ · 3H₂O 0.5 g, MgSO₄ · 7H₂O 0.5 g, FeSO₄ · 7H₂O 0.01 g, agar 18.0 g, ddwater 1,000 ml, pH 7.4-7.6 (add 25 μg/ml nalidixic acid and 100 μg/ml nystatin)

The sequence analyses based on almost full-length of the 16S rRNA gene of six potential new species_

Strain number	Name of strain having the highest 16S rRNA gene similarity	Separation medium	The highest similarity (%)	Separation temperature (°C)
T96	Agromyces binzhouensis OAct353^T	98.62	M5	25
T105	Nocardioides caeni MN8^T	98.01	M5	25
T274	Phyllobacterium zundukense Tri-48^T	98.57	M8	25
T786	Neorhizobium vignae CCBAU 05176^T	98.70	R	4
T808	Pararhizobium herbae CCBAU 83011^T	98.79	M5	4
T830	Hymenobacter humi DG31A^T	98.60	F1	4

Genera distributed in each of the four phyla_

Actinobacteria		Proteobacteria	Firmicutes	Bacteroidetes
Actinoplanes	Micrococcus	Kaistia	Bacillus	Hymenobacter
Aeromicrobium	Micromonospora	Luteimonas	Exiguobacterium
Agromyces	Nocardia	Neorhizobium	Macrococcus
Arthrobacter	Nocardioides	Pararhizobium	Paenibacillus
Dietzia	Paenarthrobacter	Phyllobacterium	Peribacillus
Glycomyces	Promicromonospora	Pseudomonas	Staphylococcus
Gordonia	Pseudarthrobacter	Pseudoxanthomonas
Kocuria	Rhodococcus	Skermanella
Kribbella	Streptomyces	Sphingopyxis
Kytococcus	Terrabacter	Variovorax
Leifsonia	Umezawaea
Longispora	Yinghuangia
Microbacterium

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region

Figures & Tables

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

BLAST results based on 16S rRNA gene sequences of 77 bacterial species_

Isolation media_

The sequence analyses based on almost full-length of the 16S rRNA gene of six potential new species_

Genera distributed in each of the four phyla_

Paradigm

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