NMDS (Non-Metric Dimensional Scaling).

<p>NMDS separates out lava cave mat communities at the phylum level, with <i>Proteobacteria</i> split out by class, from the overlying surface soils. Circles show the 95% confidence interval.</p

Plot of phyla and <i>Proteobacteria</i> class that were differentialy abundant between LABE surface soils and lava cave microbial mats.

<p>The band is the median, and the box delineates the upper and lower quartile. The whiskers show the maximum and minimum values. All data points are shown.</p

Alpha diversity indices (richness, Chao1, and Shannon).

<p>Box plots of surface soils and cave microbial mats by color. Surface soil samples are in blue and cave samples in red.</p

Scanning electron micrographs of LABE cave white and yellow microbial mats.

<p>(A) White microbial mat from Cave L-V460 showing filaments covered with putative pili/fimbrae with spheroid shapes emerging from the ends. (B) Close-up of these morphologies from A. (C) Overview of a field of these morphologies in the same white microbial mat from Cave L-V460. (D) Yellow microbial mat from Hopkins Chocolate Cave showing similar morphologies to those seen in images A-C, and including some biofilm and smooth filaments. (E) Overview of a yellow colony from Cave S-L280, showing extensive biofilm in the background and on colony edges. Beads-on-a-string morphologies are observed lying on the background biofilm. (F) Close-up of beads-on-a-string morphology on biofilm from Cave S-L280 yellow microbial mat.</p

Overview of some of the lava cave sampling sites and caves, plus a view of the surface terrain at Lava Beds National Monument, CA (LABE).

<p>(A) Entrance to Valentine Cave. (B) Surface samples taken above Hopkins Chocolate Cave. (C) Yellow microbial mat sampling site in Valentine Cave. (D) Extensive yellow microbial mats on walls of Hopkins Chocolate Cave. (E) Passage in Valentine Cave showing less microbial mat coverage near the entrance. (F) Tan microbial mat sample taken in L-V460 Cave. Photos copyright Kenneth Ingham (A, D, E) and Diana Northup (B, C, F).</p

Staggered bar chart of relative abundance of OTUs.

<p>Major and minor phyla by all cave samples and all surface samples. Cave samples have a greater relative abundance of <i>Actinobacteria</i> and <i>Nitrospirae</i>.</p

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

<div><p>Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. <i>Actinobacteria</i> dominated in all cave samples, with 39% from caves and 21% from surface soils. <i>Proteobacteria</i> made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were <i>Nitrospirae</i> (7%) followed by minor phyla (7%), compared to surface soils with <i>Bacteroidetes</i> (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community.</p></div

Characteristics of the seven study cave sites in LABE.

<p>Characteristics of the seven study cave sites in LABE.</p

Cave samples bymat color and environmental characteristics in the cave.

<p>Cave samples bymat color and environmental characteristics in the cave.</p

Percent OTUs by lowest level of classification (family or genus).

<p>(A) mean surface soils and (B)mean cave microbial mats.</p