Table 2 Phylotypes of nifH homologs obtained from different samples (Niphargus frasassianus, Niphargus montanarius, Beggiatoa-dominated biofilms and sulfidic sediment) collected at different sites in the Frasassi cave complex

From: Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem

Sample

Phylotypes

Phylogenetic group

cDNA or DNA clones/library

Genotypes a

Niphargus spp.

 N. frasassianus (ST) total RNA

Thio1a

γ-Proteobacteria (I)

14/15

HF565531–38

 

Thio1b

γ-Proteobacteria (I)

1/15

HF565539

 N. frasassianus (ST) legs DNA

Thio1a

γ-Proteobacteria (I)

2/8

HF565540

 

Thio1d

γ-Proteobacteria (I)

3/8

HF565541–43

 

Thio1e

γ-Proteobacteria (I)

3/8

HF565544–46

 N. frasassianus (RS) legs DNA

Thio1a

γ-Proteobacteria (I)

3/8

HF565555–57

 

Thio1c

γ-Proteobacteria (I)

1/8

HF565558

 

Thio1d

γ-Proteobacteria (I)

1/8

HF565560

 

Thio1e

γ-Proteobacteria (I)

2/8

HF565559, HF565561

 

Geob

Geobacter (I)

1/8

HF565569

 N. montanarius A (BG) legs DNA

Thio1a

γ-Proteobacteria (I)

6/9

HF565547–51

 

Thio1c

γ-Proteobacteria (I)

2/9

HF565552–53

 

Thio1d

γ-Proteobacteria (I)

1/9

HF565554

 N. montanarius B (BG) legs DNA

Thio1a

γ-Proteobacteria (I)

3/7

HF565562

 

Thio1c

γ-Proteobacteria (I)

3/7

HF565563–65

 

Thio1d

γ-Proteobacteria (I)

1/7

HF565566

Beggiatoa-dominated biofilm

 PC-BeggA total RNA

Desulfo1a

Desulfovibrio (III)

15/22

HF565524–27

 

Desulfo1b

Desulfovibrio (III)

1/22

HF565511

 

Desulfo1d

Desulfovibrio (III)

1/22

HF565529

 

Begg

Beggiatoa (I)

3/22

HF565530

 

Geob

Geobacter (I)

2/22

HF565569

 PC-BeggC total RNA

Desulfo1a

Desulfovibrio (III)

22/28

HF565513–23

 

Desulfo1c

Desulfovibrio (III)

1/28

HF565528

 

Desulfo2

Desulfovibrio (III)

1/28

HF565512

 

Begg

Beggiatoa (I)

4/28

HF565530

Sulfidic sediment

 PC-SedD total RNA

Thio2

γ-Proteobacteria (I)

10/30

HF565567

 

Azoarc

Azoarcus (I)

4/30

HF565568

 

Geob

Geobacter (I)

12/30

HF565569

 

Desulfo3

Desulfovibrio (III)

4/30

HF565570

  1. The abundance of each phylotype (derived from cDNA or DNA) and the GenBank accession numbers of the corresponding genotypes are provided. Abbreviations of collection locations within the Frasassi caves are provided in parentheses; see Table 1 for full names. For phylogenetic positions of individual phylotypes, see Figure 2. In parentheses are the phylogenetic assignments (I or III) to the existing nifH groups (Zehr et al., 2003b).
  2. aFor sequences showing the same amino-acid signature, representative sequences were submitted to GenBank. When nearly identical genotypes were obtained from two different samples, representatives from both libraries were submitted—such genotypes usually had >99% DNA sequence similarity.