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

Abstract

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. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (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.

In Situ Cultured Bacterial Diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada

“…These cave microorganisms were thought to be introduced from the surface by air currents, sediments, water, animal, or human vectors, which was unusual for subsurface habitats [3]. However, the cave microbial composition varied between the types and the nature of caves [4][5][6].…”

Microbial Diversity and Phylogenetic Studies of Some Microbes Obtained From Unexplored Caves of Saudi Arabia

“…During study, obtained mat colours (Table 1) were gray, tan, yellow, brown and white. Similarly, tan, white, and yellow colours were reported by Lavoie et al (2017). At the bingeing, dry and wet bulb temperatures (ᵒC) and Barometric pressure (mbar) were measured in January and used to calculate percentage of relative humidity RH).…”

“…They reported a variation in bacterial composition, species abundance and diversity among the five caves studied and the lowest richness was found for Sand town cave. Lavoie et al (2017) studied lava cave microbial diversity of subsurface mats and surface soils using 16S rDNA. They noticed the same genera for both surface soils and cave microbial mats and actinobacteria dominated in all cave samples.…”

“…These results are in agreement with the findings of present study. Microbial diversity of caves was evaluated and further work on cave environments and their microbes are needed (Al'Abri, 2011;Almalki, 2012;Lavoie et al, 2017).…”

Electron donor‐driven bacterial and archaeal community patterns along forest ring edges in Ontario, Canada

“…In the Bean ring samples, OTU1 classified as Geobacter was the most abundant in the Bean ring samples, comprising 0.03%-27.44% of all reads (Table 2). Also highly abundant, especially in the Bean ring transect 2 (2.19%-7.26%), was a sequence related to 0319-6A21, an uncultured bacterium of the class Nitrospirales, which is thought to be involved in nitrification (Lavoie et al, 2017). The third most abundant OTU may also be linked to the nitrogen cycle, as it was related to the Deltaproteobacterial taxon 43F-1404R, which has been suggested to carry out denitrification (Rasigraf et al, 2017).…”