Supplementary Table 1 The different media used in this study for isolation of bacteria from cold desert.
S. N / Media and composition per liter1. / Nutrient agar: 5 g peptone; 5 g NaCl; 3 g beef extract; 20 g agar
2. / T3 agar: 3 g Tryptone; 2 g Tryptose; 1.5 g Yeast Extract; 0.005 g MnCl2 ; 0.05 Sodium Phosphate; 20 g agar; pH-6.8
3. / Soil extract agar: 2 g glucose; 1 g Yeast Extract; 0.5 g K2HPO4; 100ml Soil extract*; 20 g agar; pH-7.2
4. / Tryptic soy agar: 17 g tryptone; 3 g soya meal; 2.5 g dextrose; 5 g NaCl; 2.5 g K2HPO4; 20 g agar; pH-7.2
5. / King’s B agar: 20 g Protease Peptone; 1.5 g K2HPO4; 1.5 MgSO4.7H2O; 10 ml Glycerol; 20 g agar; pH 7.2
6. / Jensen’s agar: 20 g Sucrose;1 g K2HPO4; 0.5 g Mg2SO4 ; 0.5 g NaCl; 0.001 g Na2MoO4; 0.01 g FeSO4; 2 g CaCO3; 20 g agar; pH 7.2
7. / R2 agar; 0.5 g Proteose peptone; 0.5 g Casmino acids; 0.5 g Yeast extract; 0.5 g Dextrose; 0.5 g Soluble starch; 0.3 g Dipotassium phosphate; 0.05 g Magnesium sulphate 7H2O; 0.3 g Sodium pyruvate; agar 20 g agar; pH 7.2 ± 0.2
8. / Chemically defined medium: 5 g casamino acids; 5 g yeast extract; 1 g sodium glutamate; 3 g tri-sodium citrate; 20 g MgSO4; 2 g KCl; 100 g NaCl; 36 mg FeCl2; 0.36 mg MgCl2; 20 g agar pH-7.0-7.2
9. / Standard growth media;7.5 g Casamino Acids; 4 g MgSO4; 2 g KCl; 150 g NaCl; 3 g Tri-Sodium citrate; 2.3 mg FeCl2;7 mg CaCl2; 0.044 mg MnSO4; 0.05 mg CuSO4; 20 g agar; pH 7.2
10. / Halophilic medium: 100 g NaCl; 2 g KCl; 1 g MgSO4·7H2O; 0.36 g CaCl2·2H2O; 0.23 g NaBr; 0.06 g NaHCO3; 5 g protease-peptone; 10 g yeast extract; 1g glucose; trace FeCl3; 20 g agar; pH 7.2–7.4
*Soil extract: 250 g soil from sampling site + 1L H20, Autoclave and filter
Supplementary Table 2 Total viable count of bacteria in water and sediment samples from Leh Ladakh on different growth media.
Sites / Type of samples / Total viable count (cfu g-1 sediment or ml-1 water × 106) on different media / No of isolates / Total isolates / No of clusters*NA / T3A / SEA / TSA / KB / JA / R2A / CDM / SGM / HM
Khardungla Pass / Soil / 5.12 / 0.011 / 1.34 / 5.68 / 0.90 / 0.09 / 0.78 / 0.005 / 0.003 / 0.008 / 62 / 32
Indus river / Water / 4.85 / 0.009 / 0.82 / 3.59 / 0.78 / 0.68 / 0.83 / 0.004 / 0.001 / 0.002 / 20
Sediment / 5.55 / 0.015 / 1.12 / 5.56 / 0.98 / 0.96 / 0.88 / 0.008 / 0.003 / 0.004 / 27
Average / 5.20 / 0.012 / 0.97 / 4.58 / 0.88 / 0.08 / 0.86 / 0.006 / 0.002 / 0.003 / 47 / 26
I-Z confluence / Water / 3.96 / 0.01 / 0.98 / 3.2 / 0.84 / 0.02 / 0.62 / 0.0073 / 0.001 / 0.0045 / 15
Sediment / 5.39 / 0.016 / 1.23 / 5.6 / 1.12 / 0.05 / 0.63 / 0.0092 / 0.0015 / 0.0098 / 28
Average / 4.68 / 0.013 / 1.10 / 4.40 / 0.98 / 0.04 / 0.60 / 0.008 / 0.001 / 0.007 / 43 / 25
Zanskar river / Water / 2.98 / 0.007 / 1.19 / 3.95 / 0.89 / 0.045 / 0.52 / 0.001 / 0.001 / 0.0006 / 16
Sediment / 4.8 / 0.015 / 1.45 / 5.26 / 1.35 / 0.081 / 0.56 / 0.005 / 0.003 / 0.0021 / 20
Average / 3.89 / 0.011 / 1.32 / 4.6 / 1.1 / 0.06 / 0.54 / 0.003 / 0.002 / 0.001 / 36 / 23
Pangong Lake / Water / 4.82 / 0.014 / 1.01 / 5.98 / 0.98 / 0.098 / 1.68 / 0.011 / 0.012 / 0.0082 / 38
Sediment / 6.33 / 0.021 / 1.98 / 7.25 / 1.69 / 0.15 / 0.87 / 0.013 / 0.016 / 0.018 / 47
Average / 5.58 / 0.018 / 1.50 / 6.62 / 1.34 / 0.12 / 1.28 / 0.012 / 0.014 / 0.013 / 85 / 40
Chumathang
/ Soil / 2.90 / 0.012 / 0.96 / 3.46 / 1.14 / 0.03 / 0.62 / 0.002 / 0.002 / 0.003 / 52 / 29Nutrient agar (NA); T3 agar (T3A); Soil extract agar (SEA); Tryptic soy agar (TSA); King’s B agar (KB); Jensen’s agar (JA);
R2 agar (R2A); Chemically defined medium (CDM); Standard growth media (SGM); Halophilic medium (HM).
*No of clusters after digestion with three restriction enzymes -AluI, HaeIII and MspI
Supplementary table 3 Distribution of bacteria from different site showing niche specificity and their phenotypic characterizations
Strain name / Nearest phylogenetic relative / Sampling sites and number of isolated bacteria / Phenotypic characteristicsKP / IR / IZ / ZR / PL / LC / Pigmentation
/color / Temp
Range (optimum) / NaCl
Tolerance (%) / pH range
IARI-L-120 / Arthrobacter sp.(DQ310481) / 3 / 2 / 2 / 1 / 2 / 1 / Bright yellow / 0-20 (12) / 5 / 6-9
IARI-L-16 / Arthrobacter sulfonivorans (FM955888) / 2 / 1 / 1 / 2 / 3 / - / Light yellow / 0-20 (12) / 5 / 6-9
IARI-L-60 / Arthrobacter sulfureus (AY392127) / 3 / 2 / 2 / - / 2 / 1 / Yellow / 0-20 (12) / 5 / 6-9
IARI-ABL-35 / Brachybacterium sp.(HQ407433) / 2 / 1 / 2 / 1 / 3 / - / Red / 4-37 (18) / 10 / 6-9
IARI-ABL-30 / Cellulosimicrobium cellulans (EU931556) / - / - / - / - / - / 2 / Creamy white / 4-37 (16) / 7 / 6-9
IARI-ABL-2 / Citricoccus sp.(AB594473) / - / - / - / 2 / - / - / Yellow / 4-37 (18) / 10 / 6-8
IARI-ABL-31 / Kocuria kristinae (AB616677) / - / 3 / - / - / - / - / Light yellow / 4-37 (18) / 10 / 6-9
IARI-ABL-32 / Kocuria palustris (HM218471) / - / 2 / - / - / - / - / Yellow / 4-37 (16) / 10 / 6-8
IARI-L-33 / Sanguibacter antarcticus (JX869974) / 3* / - / - / - / - / - / Yellow / 0-20 (10) / 3 / 5-9
IARI-ABL-45 / Flavobacterium antarcticum (FM163401) / - / - / - / - / 3 / - / Yellow / 4-30 (14) / 5 / 6-8
IARI-ABL-47 / Sphingobacterium sp. (KC252807) / - / - / - / - / 5 / - / Yellow / 4-30 (14) / 5 / 6-8
IARI-L-24 / Bacillus anthracis (JN999848) / - / - / - / - / - / 1 / Cream / 4-30 (16) / 5 / 5-9
IARI-ABL-36 / Bacillus baekryungensis (JN210568) / - / - / - / - / 3 / - / Off white / 4-30 (16) / 10 / 5-9
IARI-L-73 / Bacillus cereus (JX155390) / 2 / 2 / 1 / 1 / 2 / 1 / Light yellow / 4-30 (16) / 5 / 5-9
IARI-L-21 / Bacillus firmus (GQ903380) / 2 / 1 / 2 / 1 / 3 / 1 / Yellow / 0-30 (14) / 10 / 5-9
IARI- ABL-37 / Bacillus flexus (GU397395) / 1 / 2 / 2 / 2 / 3 / 1 / Off white / 4-37 (16) / 7 / 5-9
IARI- ABL-38 / Bacillus licheniformis (GQ280023) / 2 / 1 / - / 1 / 1 / 1 / Creamy / 4-37 (18) / 7 / 6-9
IARI- ABL-39 / Bacillus marisflavi (AB617551) / - / - / - / - / 3 / - / Bright white / 4-37 (16) / 10 / 5-9
IARI- ABL-40 / Bacillus mojavensis (JF901760) / 2 / - / - / 2 / 3 / 1 / Yellow / 4-37 (16) / 10 / 5-11
IARI-L-74 / Bacillus muralis (JX035939) / 2 / - / 1 / - / 2 / 1 / Cream / 0-20 (10) / 5 / 5-9
IARI-L-54 / Bacillus pumilus (JF803782) / 2 / 1 / 1 / 2 / 2 / 1 / White / 4-30 (16) / 5 / 5-8
IARI-L-118 / Bacillus simplex (DQ514314) / 3 / - / 2 / 1 / 2 / - / White / 0-30 (14) / 3 / 6-9
IARI-L-14 / Bacillus sp.(JQ956513) / 2 / - / 2 / 1 / 2 / - / Cream / 4-30 (14) / 5 / 5-9
IARI-L-69 / Bacillus subtilis (GU125629) / 1 / 2 / 2 / 1 / 1 / 3 / White / 0-30 (14) / 3 / 5-9
IARI-L-46 / Desemzia incerta (HQ336336) / 2 / - / - / - / 1 / - / White / 4-30 (14) / 5 / 6-8
IARI-L-70 / Exiguobacterium antarcticum (NR043476) / - / - / - / 2 / 4 / 3 / Bright orange / 0-20 (12) / 3 / 6-9
IARI-L-62 / Exiguobacterium sp.(DQ019169) / 1 / 2 / - / 2 / 2 / 1 / Orange / 0-20 (10) / 3 / 6-9
IARI-L-116 / Exiguobacterium undae (FN870073) / 2 / 2 / 2 / - / 1 / 3 / Orange / 0-20 (10) / 3 / 6-8
IARI-L-2 / Lysinibacillus fusiformis (EU187498) / 3 / 2 / 3 / 1 / 3 / - / Peach / 4-30 (16) / 3 / 6-9
IARI-L-65 / Lysinibacillus sp.(GQ199724) / - / - / 1 / - / 2 / 2 / Peach / 4-30 (16) / 3 / 5-8
IARI-L-3 / Lysinibacillus sphaericus (JX067902) / - / - / 1 / - / - / - / Peach / 4-30 (16) / 3 / 6-8
IARI-L-128 / Paenibacillus sp.(JF694817) / 2 / 1 / 2 / 2 / 1 / 2 / Creamy white / 4-30 (16) / 5 / 5-9
IARI-L-127 / Paenibacillus terrae (EF690404) / 2 / - / - / - / - / - / Cream / 0-30 (14) / 3 / 6-9
IARI-L-76 / Paenibacillus xylanexedens (NR044524) / - / - / - / - / - / 3 / Cream / 0-20 (10) / 5 / 5-9
IARI-ABL-9 / Planococcus antarcticus (FR691465) / - / - / - / - / 1 / - / Orange / 0-20 (12) / 10 / 5-11
IARI-L-39 / Planococcus donghaensis (NR_044073) / 1 / - / - / - / 1 / - / Orange / 0-20 (12) / 5 / 6-9
IARI-ABL-3 / Planococcus kocurii (AB680986) / 1 / - / 2 / - / 2 / 2 / Light orange / 4-30 (16) / 7 / 6-9
IARI- ABL-41 / Pontibacillus sp. (AB305321) / - / 2 / - / - / 1 / - / Yellow / 4-30 (16) / 10 / 5-9
IARI-ABL-18 / Sinobaca beijingensis (DQ344635) / - / - / - / 3 / - / - / Red / 4-30 (16) / 10 / 5-11
IARI-L-77 / Sporosarcina aquimarina (FJ944660) / 1 / - / - / - / 2 / - / Bright orange / 0-20 (12) / 10 / 5-9
IARI-ABL-33 / Staphylococcus arlettae (JN315890) / - / - / 2 / - / - / - / Off white / 4-30 (16) / 10 / 5-9
IARI-ABL-26 / Aurantimonas altamirensis (AB682666) / - / - / - / - / 2 / - / Bright yellow / 4-30 (16) / 10 / 5-8
IARI-ABL-27 / Brevundimonas terrae (NR043726) / - / - / - / - / - / 3 / Light yellow / 4-37 (18) / 10 / 6-11
IARI-ABL-28 / Paracoccus sp.(AY864654) / - / - / - / - / - / 3 / Orange / 4-37 (18) / 5 / 5-8
IARI-L-110 / Janthinobacterium sp.(GU244366) / 2 / 2 / - / - / 1 / 2 / Light black / 0-30 (14) / 3 / 5-8
IARI-L-23 / Alishewanella sp. (EU574916.) / 3 / 2 / - / 2 / 3 / 2 / Off white / 0-30 (14) / 3 / 5-8
IARI-ABL-29 / Klebsiella sp. (GU290319) / - / - / - / 2 / - / - / Cream / 4-37 (18) / 7 / 5-8
IARI-L-6 / Providencia sp. (HM468083) / 2 / 1 / 2 / 1 / 2 / 2 / Peach / 0-30 (14) / 5 / 6-9
IARI-L-28 / Pseudomonas frederiksbergensis (JF343187) / - / - / - / - / - / 2 / Pink / 0-30 (14) / 3 / 6-9
IARI-L-117 / Pseudomonas peli (HM371423) / 2 / 2 / 2 / - / 2 / 2 / Yellow / 0-30 (14) / 3 / 6-9
IARI-L-109 / Pseudomonas putida (AF094742) / 1 / 2 / 2 / - / 2 / 2 / Yellow / 0-30 (14) / 3 / 6-8
IARI-L-108 / Pseudomonas reactans (JF343208) / 2 / 2 / 1 / 1 / 1 / 2 / Yellow / 0-30 (14) / 5 / 5-9
IARI-L-71 / Pseudomonas sp. (AM403657) / 2 / 2 / 2 / - / 2 / 1 / Cream / 4-30 (16) / 3 / 6-8
IARI-L-119 / Pseudomonas stutzeri (EF429003) / 1 / 2 / 1 / - / 1 / - / Red / 0-20 (8) / 3 / 5-8
IARI-L-112 / Psychrobacter glacincola (AY771724) / - / - / - / - / 3 / - / White / 0-20 (10) / 3 / 6-8
IARI-ABL-34 / Stenotrophomonas maltophilia (GU737688) / - / 3 / - / - / - / - / Off white / 4-37 (18) / 10 / 6-11
IARI-L-9 / Vibrio metschnikovii (NR029258) / - / - / - / 2 / - / - / Orange / 4-30 (16) / 3 / 6-9
Number of clusters (175) / 32 / 26 / 25 / 23 / 40 / 29
Number of isolates (325) / 62 / 47 / 43 / 36 / 85 / 52
Khardungla Pass (KP); Indus River (IR); I-Z confluence (IZ); Zanskar River (ZR); Pangong Lake (PL); Chumathang (LC); *Niche-specific bacteria