Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

Abstract

This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the order Thermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA identity of one archaeon is only 91.6% compared to the most closely related isolate Thermogymnomonas acidicola. Hence, this organism is the first member of a new genus. The enrichment culture is dominated by this microorganism and the ARMAN. The third archaeon in the community seems to be present in minor quantities and has a 100% 16S rRNA identity to the recently isolated Cuniculiplasma divulgatum. The enriched ARMAN species is most probably incapable of sugar metabolism because the key genes for sugar catabolism and anabolism could not be identified in the metagenome. Metatranscriptomic analysis suggests that the TCA cycle funneled with amino acids is the main metabolic pathway used by the archaea of the community. Microscopic analysis revealed that growth of the ARMAN is supported by the formation of cell aggregates. These might enable feeding of the ARMAN by or on other community members.

Machine-assisted cultivation and analysis of biofilms

“…Using CARD-FISH and 16S-rRNA analysis, we found that fluidic cultivation was successful. Indeed this technique enabled the cultivation of the first co-culture that contained only an ARMAN species along with a single helper organism (Figure 4 d), dubbed as B_DKE that we had previously observed in the more complex co-culture obtained by conventional cultivation techniques 30 . Most likely, B_DKE is necessary as producer for compounds that cannot be produced by the multi-auxotrophic ARMAN organism.…”

“…Therefore, fluidic cultivation of a stable laboratory culture of anaerobic acidophilic nanoorganisms 30 was conducted. This ARMAN co-culture was derived from the aforementioned acidophilic environmental AMD biofilm (shown in Figure 4 a) and evolution by several transfers in anoxic medium under planktonic conditions led to a community that was composed of three novel archaea including an ARMAN species and a fungus 30 (Figure 4 c). We used this co-culture as inoculum for microfluidic cultivation inside the anoxic gasket.…”

CAMITAX: Taxon labels for microbial genomes

“…Metagenome-assembled genomes (MAGs) on the other hand rarely contain full-length 16S rRNA genes [44,45]. While there are notable exceptions to this rule [46,47], the above assignment strategies are generally not expected to work well for today's SAGs and MAGs.…”

An archaeal symbiont-host association from the deep terrestrial subsurface

“…S1. (167,168,171,174) amino acids (71, 110-117, 120-128, 130-141, 144-166, 175-178) G1P (precursor for activated sugars) (42)(43)(44)(45)(46)(47)(48)(49)(50) activated sugars (185-209, 97, 215) glycogen (193,185,214) molecular building blocks via acetyl-CoA (36-39) IPP (87-91), pyruvate (41), DHAP (42)(43)(44)(45)(46)(47) AdoCbl (179-184) NAD(P)H (10)(11)(12)(13)(14)(15)(16), FADH 2 (3)(4)(5)(6)(7)(8)(9) PLP (1) THF derivate (17,18,(20)(21)(22)(23)(24)(25) red. ferredoxin (18,216) NTPs (51-69, 71-77, 80, 82) dNTPs (69, 70, 77, 79, 81, 82) ATP GTP (83,220) energy demanding processes synthesis of activated sugar glycogen degrataion (210), synthesis of activated sugars (186, 192-194, 196, 198, 203, 205, 207, 215), transfer of glycosyl gropus (229) lipid biosynthesis…”

“…These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.The DPANN (Diapherotrites, Parvarchaeota, Aigarchaeota, Nanoarchaeota, Nanohaloarchaeota) [1] radiation is a proposed monophyletic group of diverse archaeal phyla whose organisms exhibit mainly reduced genomes with limited metabolic capacities [2]. While most of these archaea were suggested to live in symbiosis with other microorganisms, respective hosts were only described for Nanoarchaeota [3,4] and Micrarchaeota (ARMAN) symbionts [5][6][7]. However, no DPANN-host interaction has been described for representatives in aquifer systems, where these archaea are particularly abundant and very diverse [2].Recently, subsurface fluids discharged by a cold, CO2-driven geyser at the Colorado Plateau, Utah (Crystal Geyser) revealed the presence of multiple novel archaeal organisms,…”